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Identification of a Carbapenemase-Producing Hypervirulent Klebsiella pneumoniae Isolate in the United States.

Karlsson M, Stanton RA, Ansari U, McAllister G, Chan MY, Sula E, Grass JE, Duffy N, Anacker ML, Witwer ML, Rasheed JK, Elkins CA, Halpin AL.

Antimicrob Agents Chemother. 2019 Jun 24;63(7). pii: e00519-19. doi: 10.1128/AAC.00519-19. Print 2019 Jul.


Draft Genome Sequences of 72 Isolates from All Four Species of Shigella.

Gangiredla J, Mammel MK, Lacher DW, Tartera C, Jackson SA, Patel IR, Elkins CA, Mukherjee A.

Microbiol Resour Announc. 2018 Nov 29;7(21). pii: e01399-18. doi: 10.1128/MRA.01399-18. eCollection 2018 Nov.


Draft Genome Sequences of the Escherichia coli Reference (ECOR) Collection.

Patel IR, Gangiredla J, Mammel MK, Lampel KA, Elkins CA, Lacher DW.

Microbiol Resour Announc. 2018 Oct 11;7(14). pii: e01133-18. doi: 10.1128/MRA.01133-18. eCollection 2018 Oct.


A Vegetable Fermentation Facility Hosts Distinct Microbiomes Reflecting the Production Environment.

Einson JE, Rani A, You X, Rodriguez AA, Randell CL, Barnaba T, Mammel MK, Kotewicz ML, Elkins CA, Sela DA.

Appl Environ Microbiol. 2018 Oct 30;84(22). pii: e01680-18. doi: 10.1128/AEM.01680-18. Print 2018 Nov 15.


Interlaboratory Evaluation of the U.S. Food and Drug Administration Escherichia coli Identification Microarray for Profiling Shiga Toxin-Producing Escherichia coli.

Patel IR, Gangiredla J, Lacher DW, Mammel MK, Bagi L, Baranzoni GM, Fratamico PM, Roberts EL, DebROY C, Lindsey RL, V Stoneburg D, Martin H, Smith P, Strockbine NA, Elkins CA, Scheutz F, Feng PCH.

J Food Prot. 2018 Aug;81(8):1275-1282. doi: 10.4315/0362-028X.JFP-18-052.


Fifty-Six Draft Genome Sequences of 10 Lactobacillus Species from 22 Commercial Dietary Supplements.

Gangiredla J, Barnaba TJ, Mammel MK, Lacher DW, Elkins CA, Lampel KA, Whitehouse CA, Tartera C.

Genome Announc. 2018 Jun 28;6(26). pii: e00621-18. doi: 10.1128/genomeA.00621-18.


Draft Genome Sequences of Bifidobacterium Strains Isolated from Dietary Supplements and Cultured Food Products.

Barnaba TJ, Gangiredla J, Mammel MK, Lacher DW, Elkins CA, Lampel KA, Whitehouse CA, Tartera C.

Genome Announc. 2018 Jun 28;6(26). pii: e00610-18. doi: 10.1128/genomeA.00610-18.


Draft Genome Sequences of Escherichia albertii, Escherichia fergusonii, and Strains Belonging to Six Cryptic Lineages of Escherichia spp.

Gangiredla J, Mammel MK, Barnaba TJ, Tartera C, Gebru ST, Patel IR, Leonard SR, Kotewicz ML, Lampel KA, Elkins CA, Lacher DW.

Genome Announc. 2018 May 3;6(18). pii: e00271-18. doi: 10.1128/genomeA.00271-18.


DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces.

Shridhar PB, Patel IR, Gangiredla J, Noll LW, Shi X, Bai J, Elkins CA, Strockbine N, Nagaraja TG.

PLoS One. 2018 Apr 30;13(4):e0196490. doi: 10.1371/journal.pone.0196490. eCollection 2018.


Genetic Analysis of Virulence Potential of Escherichia coli O104 Serotypes Isolated From Cattle Feces Using Whole Genome Sequencing.

Shridhar PB, Patel IR, Gangiredla J, Noll LW, Shi X, Bai J, Elkins CA, Strockbine NA, Nagaraja TG.

Front Microbiol. 2018 Mar 1;9:341. doi: 10.3389/fmicb.2018.00341. eCollection 2018.


Species-Wide Collection of Escherichia coli Isolates for Examination of Genomic Diversity.

Gangiredla J, Mammel MK, Barnaba TJ, Tartera C, Gebru ST, Patel IR, Leonard SR, Kotewicz ML, Lampel KA, Elkins CA, Lacher DW.

Genome Announc. 2017 Dec 14;5(50). pii: e01321-17. doi: 10.1128/genomeA.01321-17.


Draft Genome Sequences of Ciprofloxacin-Resistant Salmonella enterica Strains with Multiple-Antibiotic Resistance, Isolated from Imported Foods.

Khan AA, Khajanchi BK, Khan SA, Elkins CA, Foley SL.

Genome Announc. 2017 Nov 9;5(45). pii: e01222-17. doi: 10.1128/genomeA.01222-17.


Application of next generation sequencing toward sensitive detection of enteric viruses isolated from celery samples as an example of produce.

Yang Z, Mammel M, Papafragkou E, Hida K, Elkins CA, Kulka M.

Int J Food Microbiol. 2017 Nov 16;261:73-81. doi: 10.1016/j.ijfoodmicro.2017.07.021. Epub 2017 Aug 3.


Complete Genome Sequence of a Human Sapovirus GI.2 Variant, Isolated from a Patient in Ireland in 2016.

Yang Z, O'Gorman J, De Gascun C, Bennett C, Elkins CA, Kulka M, Coughlan S.

Genome Announc. 2017 Sep 21;5(38). pii: e01028-17. doi: 10.1128/genomeA.01028-17.


Draft Genome Sequences of Escherichia coli O104 Strains of Bovine and Human Origin.

Shridhar PB, Patel IR, Gangiredla J, Mammel MK, Noll L, Shi X, Bai J, Elkins CA, Strockbine N, Nagaraja TG.

Genome Announc. 2017 Aug 17;5(33). pii: e00630-17. doi: 10.1128/genomeA.00630-17.


Use of the Escherichia coli Identification Microarray for Characterizing the Health Risks of Shiga Toxin-Producing Escherichia coli Isolated from Foods.

Lacher DW, Gangiredla J, Patel I, Elkins CA, Feng PC.

J Food Prot. 2016 Oct;79(10):1656-1662. doi: 10.4315/0362-028X.JFP-16-176.


Human Gut-On-A-Chip Supports Polarized Infection of Coxsackie B1 Virus In Vitro.

Villenave R, Wales SQ, Hamkins-Indik T, Papafragkou E, Weaver JC, Ferrante TC, Bahinski A, Elkins CA, Kulka M, Ingber DE.

PLoS One. 2017 Feb 1;12(2):e0169412. doi: 10.1371/journal.pone.0169412. eCollection 2017.


Strain-Level Discrimination of Shiga Toxin-Producing Escherichia coli in Spinach Using Metagenomic Sequencing.

Leonard SR, Mammel MK, Lacher DW, Elkins CA.

PLoS One. 2016 Dec 8;11(12):e0167870. doi: 10.1371/journal.pone.0167870. eCollection 2016.


Complete Genome Sequence of Human Norovirus Strain GII.P7-GII.6 Detected in a Patient in the United States in 2014.

Yang Z, Vinjé J, Elkins CA, Kulka M.

Genome Announc. 2016 Oct 20;4(5). pii: e01211-16. doi: 10.1128/genomeA.01211-16.


Towards next-generation sequencing analytics for foodborne RNA viruses: Examining the effect of RNA input quantity and viral RNA purity.

Yang Z, Leonard SR, Mammel MK, Elkins CA, Kulka M.

J Virol Methods. 2016 Oct;236:221-230. doi: 10.1016/j.jviromet.2016.07.013. Epub 2016 Jul 18.


Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing.

Patro JN, Ramachandran P, Barnaba T, Mammel MK, Lewis JL, Elkins CA.

mSphere. 2016 Mar 30;1(2). pii: e00057-16. doi: 10.1128/mSphere.00057-16. eCollection 2016 Mar-Apr.


FDA Escherichia coli Identification (FDA-ECID) Microarray: a Pangenome Molecular Toolbox for Serotyping, Virulence Profiling, Molecular Epidemiology, and Phylogeny.

Patel IR, Gangiredla J, Lacher DW, Mammel MK, Jackson SA, Lampel KA, Elkins CA.

Appl Environ Microbiol. 2016 May 16;82(11):3384-3394. doi: 10.1128/AEM.04077-15. Print 2016 Jun 1.


Genomic evidence reveals numerous Salmonella enterica serovar Newport reintroduction events in Suwannee watershed irrigation ponds.

Li B, Jackson SA, Gangiredla J, Wang W, Liu H, Tall BD, Beaubrun JJ, Jay-Russell M, Vellidis G, Elkins CA.

Appl Environ Microbiol. 2015 Dec;81(24):8243-53. doi: 10.1128/AEM.02179-15. Epub 2015 Sep 18.


Application of metagenomic sequencing to food safety: detection of Shiga Toxin-producing Escherichia coli on fresh bagged spinach.

Leonard SR, Mammel MK, Lacher DW, Elkins CA.

Appl Environ Microbiol. 2015 Dec;81(23):8183-91. doi: 10.1128/AEM.02601-15. Epub 2015 Sep 18.


Genetic and resistance phenotypic subtyping of Salmonella Saintpaul isolates from various food sources and humans: Phylogenetic concordance in combinatory analyses.

Hayford AE, Brown EW, Zhao S, Mammel MK, Gangiredla J, Abbott JW, Friedman SL, Ayers SL, Lewis JL, Lacher DW, McDermott P, Elkins CA.

Infect Genet Evol. 2015 Dec;36:92-107. doi: 10.1016/j.meegid.2015.08.022. Epub 2015 Aug 20.


Development and utility of the FDA 'GutProbe' DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics.

Patro JN, Ramachandran P, Lewis JL, Mammel MK, Barnaba T, Pfeiler EA, Elkins CA.

J Appl Microbiol. 2015 Jun;118(6):1478-88. doi: 10.1111/jam.12795. Epub 2015 Apr 9.


Staphylococcus aureus toxic shock syndrome toxin-1 (TSST-1) production and Lactobacillus species growth in a defined medium simulating vaginal secretions.

Stingley RL, Liu H, Mullis LB, Elkins CA, Hart ME.

J Microbiol Methods. 2014 Nov;106:57-66. doi: 10.1016/j.mimet.2014.08.002. Epub 2014 Aug 16.


Diversity and antimicrobial resistance of Salmonella enterica isolates from surface water in Southeastern United States.

Li B, Vellidis G, Liu H, Jay-Russell M, Zhao S, Hu Z, Wright A, Elkins CA.

Appl Environ Microbiol. 2014 Oct;80(20):6355-65. doi: 10.1128/AEM.02063-14. Epub 2014 Aug 8.


Antibodies specific for nucleic acids and applications in genomic detection and clinical diagnostics.

Hu Z, Leppla SH, Li B, Elkins CA.

Expert Rev Mol Diagn. 2014 Sep;14(7):895-916. doi: 10.1586/14737159.2014.931810. Epub 2014 Jul 11. Review.


A metallo-β-lactamase is responsible for the degradation of ceftiofur by the bovine intestinal bacterium Bacillus cereus P41.

Erickson BD, Elkins CA, Mullis LB, Heinze TM, Wagner RD, Cerniglia CE.

Vet Microbiol. 2014 Aug 27;172(3-4):499-504. doi: 10.1016/j.vetmic.2014.05.032. Epub 2014 Jun 6.


Novel microarray design for molecular serotyping of shiga toxin- producing Escherichia coli strains isolated from fresh produce.

Lacher DW, Gangiredla J, Jackson SA, Elkins CA, Feng PC.

Appl Environ Microbiol. 2014 Aug;80(15):4677-4682.


Draft Genome Sequence of the Multidrug-Resistant Escherichia coli Strain LR09, Isolated from a Wastewater Treatment Plant.

Leonard SR, Lacher DW, Elkins CA, Jung CM.

Genome Announc. 2014 Apr 3;2(2). pii: e00272-14. doi: 10.1128/genomeA.00272-14.


Detection of live Escherichia coli O157:H7 cells by PMA-qPCR.

Li B, Hu Z, Elkins CA.

J Vis Exp. 2014 Feb 1;(84):e50967. doi: 10.3791/50967.


Development of a tiered multilocus sequence typing scheme for members of the Lactobacillus acidophilus complex.

Ramachandran P, Lacher DW, Pfeiler EA, Elkins CA.

Appl Environ Microbiol. 2013 Dec;79(23):7220-8. doi: 10.1128/AEM.02257-13. Epub 2013 Sep 13.


Genomic paradigms for food-borne enteric pathogen analysis at the USFDA: case studies highlighting method utility, integration and resolution.

Elkins CA, Kotewicz ML, Jackson SA, Lacher DW, Abu-Ali GS, Patel IR.

Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2013;30(8):1422-36. doi: 10.1080/19440049.2012.743192. Epub 2012 Dec 3.


Rapid genomic-scale analysis of Escherichia coli O104:H4 by using high-resolution alternative methods to next-generation sequencing.

Jackson SA, Kotewicz ML, Patel IR, Lacher DW, Gangiredla J, Elkins CA.

Appl Environ Microbiol. 2012 Mar;78(5):1601-5. doi: 10.1128/AEM.07464-11. Epub 2011 Dec 30.


Inhibition of Staphylococcus aureus by lysostaphin-expressing Lactobacillus plantarum WCFS1 in a modified genital tract secretion medium.

Liu H, Gao Y, Yu LR, Jones RC, Elkins CA, Hart ME.

Appl Environ Microbiol. 2011 Dec;77(24):8500-8. doi: 10.1128/AEM.06755-11. Epub 2011 Oct 7.


A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.

Strader MB, Costantino N, Elkins CA, Chen CY, Patel I, Makusky AJ, Choy JS, Court DL, Markey SP, Kowalak JA.

Mol Cell Proteomics. 2011 Mar;10(3):M110.005199. doi: 10.1074/mcp.M110.005199. Epub 2010 Dec 17.


Interaction of dietary resveratrol with animal-associated bacteria.

Jung CM, Heinze TM, Schnackenberg LK, Mullis LB, Elkins SA, Elkins CA, Steele RS, Sutherland JB.

FEMS Microbiol Lett. 2009 Aug;297(2):266-73. doi: 10.1111/j.1574-6968.2009.01691.x. Epub 2009 Jun 22.


Acetylation of fluoroquinolone antimicrobial agents by an Escherichia coli strain isolated from a municipal wastewater treatment plant.

Jung CM, Heinze TM, Strakosha R, Elkins CA, Sutherland JB.

J Appl Microbiol. 2009 Feb;106(2):564-71. doi: 10.1111/j.1365-2672.2008.04026.x.


Lactobacillus-mediated inhibition of clinical toxic shock syndrome Staphylococcus aureus strains and its relation to acid and peroxide production.

Elkins CA, Muñoz ME, Mullis LB, Stingley RL, Hart ME.

Anaerobe. 2008 Nov;14(5):261-7. doi: 10.1016/j.anaerobe.2008.08.003. Epub 2008 Sep 24.


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