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Using Genomics to Track Global Antimicrobial Resistance.

Hendriksen RS, Bortolaia V, Tate H, Tyson GH, Aarestrup FM, McDermott PF.

Front Public Health. 2019 Sep 4;7:242. doi: 10.3389/fpubh.2019.00242. eCollection 2019. Review.


Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates.

Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu CH, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W.

Antimicrob Agents Chemother. 2019 Oct 22;63(11). pii: e00483-19. doi: 10.1128/AAC.00483-19. Print 2019 Nov.


Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella.

Nguyen M, Long SW, McDermott PF, Olsen RJ, Olson R, Stevens RL, Tyson GH, Zhao S, Davis JJ.

J Clin Microbiol. 2019 Jan 30;57(2). pii: e01260-18. doi: 10.1128/JCM.01260-18. Print 2019 Feb.


Novel linezolid resistance plasmids in Enterococcus from food animals in the USA.

Tyson GH, Sabo JL, Hoffmann M, Hsu CH, Mukherjee S, Hernandez J, Tillman G, Wasilenko JL, Haro J, Simmons M, Wilson Egbe W, White PL, Dessai U, Mcdermott PF.

J Antimicrob Chemother. 2018 Dec 1;73(12):3254-3258. doi: 10.1093/jac/dky369.


Whole-Genome Sequence Analysis of CTX-M Containing Escherichia coli Isolates from Retail Meats and Cattle in the United States.

Tadesse DA, Li C, Mukherjee S, Hsu CH, Bodeis Jones S, Gaines SA, Kabera C, Loneragan GH, Torrence M, Harhay DM, McDermott PF, Zhao S.

Microb Drug Resist. 2018 Sep;24(7):939-948. doi: 10.1089/mdr.2018.0206. Epub 2018 Aug 27.


Antimicrobial Resistance in Nontyphoidal Salmonella.

McDermott PF, Zhao S, Tate H.

Microbiol Spectr. 2018 Jul;6(4). doi: 10.1128/microbiolspec.ARBA-0014-2017. Review.


Identification and Characterization of Conjugative Plasmids That Encode Ciprofloxacin Resistance in Salmonella.

Chen K, Dong N, Zhao S, Liu L, Li R, Xie M, Lin D, Wai-Chi Chan E, Meng J, McDermott PF, Chen S.

Antimicrob Agents Chemother. 2018 Jul 27;62(8). pii: e00575-18. doi: 10.1128/AAC.00575-18. Print 2018 Aug.


Whole-genome sequencing based characterization of antimicrobial resistance in Enterococcus.

Tyson GH, Sabo JL, Rice-Trujillo C, Hernandez J, McDermott PF.

Pathog Dis. 2018 Mar 1;76(2). doi: 10.1093/femspd/fty018.


Complete Genome Sequences of 14 Salmonella enterica Serovar Enteritidis Strains Recovered from Human Clinical Cases between 1949 and 1995 in the United States.

Tadesse DA, Hoffmann M, Sarria S, Lam C, Brown E, Allard M, McDermott PF.

Genome Announc. 2018 Jan 4;6(1). pii: e01406-17. doi: 10.1128/genomeA.01406-17.


Cloning and Expression of Novel Aminoglycoside Phosphotransferase Genes from Campylobacter and Their Role in the Resistance to Six Aminoglycosides.

Zhao S, Mukherjee S, Li C, Jones SB, Young S, McDermott PF.

Antimicrob Agents Chemother. 2017 Dec 21;62(1). pii: e01682-17. doi: 10.1128/AAC.01682-17. Print 2018 Jan.


Prevalence and Antimicrobial Resistance of Enterococci Isolated from Retail Meats in the United States, 2002 to 2014.

Tyson GH, Nyirabahizi E, Crarey E, Kabera C, Lam C, Rice-Trujillo C, McDermott PF, Tate H.

Appl Environ Microbiol. 2017 Dec 15;84(1). pii: e01902-17. doi: 10.1128/AEM.01902-17. Print 2018 Jan 1.


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.


National Antimicrobial Resistance Monitoring System: Two Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance.

Karp BE, Tate H, Plumblee JR, Dessai U, Whichard JM, Thacker EL, Hale KR, Wilson W, Friedman CR, Griffin PM, McDermott PF.

Foodborne Pathog Dis. 2017 Oct;14(10):545-557. doi: 10.1089/fpd.2017.2283. Epub 2017 Aug 9. Review.


Corrigendum: Allelic variation contributes to bacterial host specificity.

Yue M, Han X, De Masi L, Zhu C, Ma X, Zhang J, Wu R, Schmieder R, Kaushik RS, Fraser GP, Zhao S, McDermott PF, Weill FX, Mainil JG, Arze C, Fricke WF, Edwards RA, Brisson D, Zhang NR, Rankin SC, Schifferli DM.

Nat Commun. 2017 Aug 8;8:15229. doi: 10.1038/ncomms15229.


Identification of Plasmid-Mediated Quinolone Resistance in Salmonella Isolated from Swine Ceca and Retail Pork Chops in the United States.

Tyson GH, Tate HP, Zhao S, Li C, Dessai U, Simmons M, McDermott PF.

Antimicrob Agents Chemother. 2017 Sep 22;61(10). pii: e01318-17. doi: 10.1128/AAC.01318-17. Print 2017 Oct.


Comparative Analysis of Extended-Spectrum-β-Lactamase CTX-M-65-Producing Salmonella enterica Serovar Infantis Isolates from Humans, Food Animals, and Retail Chickens in the United States.

Tate H, Folster JP, Hsu CH, Chen J, Hoffmann M, Li C, Morales C, Tyson GH, Mukherjee S, Brown AC, Green A, Wilson W, Dessai U, Abbott J, Joseph L, Haro J, Ayers S, McDermott PF, Zhao S.

Antimicrob Agents Chemother. 2017 Jun 27;61(7). pii: e00488-17. doi: 10.1128/AAC.00488-17. Print 2017 Jul.


Molecular Subtyping and Source Attribution of Campylobacter Isolated from Food Animals.

Tyson GH, Tate HP, Abbott J, Tran TT, Kabera C, Crarey E, Young S, McDermott PF, Sprague G, Campbell M, Adeyemo O, Browne-Silva J, Myers M, Thitaram S, Zhao S.

J Food Prot. 2016 Nov;79(11):1891-1897. doi: 10.4315/0362-028X.JFP-16-195.


Establishing Genotypic Cutoff Values To Measure Antimicrobial Resistance in Salmonella.

Tyson GH, Zhao S, Li C, Ayers S, Sabo JL, Lam C, Miller RA, McDermott PF.

Antimicrob Agents Chemother. 2017 Feb 23;61(3). pii: e02140-16. doi: 10.1128/AAC.02140-16. Print 2017 Mar.


MRSA and multidrug-resistant Staphylococcus aureus in U.S. retail meats, 2010-2011.

Ge B, Mukherjee S, Hsu CH, Davis JA, Tran TTT, Yang Q, Abbott JW, Ayers SL, Young SR, Crarey ET, Womack NA, Zhao S, McDermott PF.

Food Microbiol. 2017 Apr;62:289-297. doi: 10.1016/ Epub 2016 Oct 18.


Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella.

McDermott PF, Tyson GH, Kabera C, Chen Y, Li C, Folster JP, Ayers SL, Lam C, Tate HP, Zhao S.

Antimicrob Agents Chemother. 2016 Aug 22;60(9):5515-20. doi: 10.1128/AAC.01030-16. Print 2016 Sep.


Antimicrobial Resistance in Salmonella in the United States from 1948 to 1995.

Tadesse DA, Singh A, Zhao S, Bartholomew M, Womack N, Ayers S, Fields PI, McDermott PF.

Antimicrob Agents Chemother. 2016 Mar 25;60(4):2567-71. doi: 10.1128/AAC.02536-15. Print 2016 Apr.


Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli.

Tyson GH, Li C, Ayers S, McDermott PF, Zhao S.

FEMS Microbiol Lett. 2016 Feb;363(4). pii: fnw009. doi: 10.1093/femsle/fnw009. Epub 2016 Jan 17.


Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

Zhao S, Tyson GH, Chen Y, Li C, Mukherjee S, Young S, Lam C, Folster JP, Whichard JM, McDermott PF.

Appl Environ Microbiol. 2015 Oct 30;82(2):459-66. doi: 10.1128/AEM.02873-15. Print 2016 Jan 15.


Allelic variation contributes to bacterial host specificity.

Yue M, Han X, De Masi L, Zhu C, Ma X, Zhang J, Wu R, Schmieder R, Kaushik RS, Fraser GP, Zhao S, McDermott PF, Weill FX, Mainil JG, Arze C, Fricke WF, Edwards RA, Brisson D, Zhang NR, Rankin SC, Schifferli DM.

Nat Commun. 2015 Oct 30;6:8754. doi: 10.1038/ncomms9754. Erratum in: Nat Commun. 2017 Aug 08;8:15229.


WGS accurately predicts antimicrobial resistance in Escherichia coli.

Tyson GH, McDermott PF, Li C, Chen Y, Tadesse DA, Mukherjee S, Bodeis-Jones S, Kabera C, Gaines SA, Loneragan GH, Edrington TS, Torrence M, Harhay DM, Zhao S.

J Antimicrob Chemother. 2015 Oct;70(10):2763-9. doi: 10.1093/jac/dkv186. Epub 2015 Jul 3.


Complete Sequences of Six IncA/C Plasmids of Multidrug-Resistant Salmonella enterica subsp. enterica Serotype Newport.

Cao G, Allard MW, Hoffmann M, Monday SR, Muruvanda T, Luo Y, Payne J, Rump L, Meng K, Zhao S, McDermott PF, Brown EW, Meng J.

Genome Announc. 2015 Feb 26;3(1). pii: e00027-15. doi: 10.1128/genomeA.00027-15.


Novel gentamicin resistance genes in Campylobacter isolated from humans and retail meats in the USA.

Zhao S, Mukherjee S, Chen Y, Li C, Young S, Warren M, Abbott J, Friedman S, Kabera C, Karlsson M, McDermott PF.

J Antimicrob Chemother. 2015 May;70(5):1314-21. doi: 10.1093/jac/dkv001. Epub 2015 Feb 1.


Characterization of antibiotic and disinfectant susceptibility profiles among Pseudomonas aeruginosa veterinary isolates recovered during 1994-2003.

Beier RC, Foley SL, Davidson MK, White DG, McDermott PF, Bodeis-Jones S, Zhao S, Andrews K, Crippen TL, Sheffield CL, Poole TL, Anderson RC, Nisbet DJ.

J Appl Microbiol. 2015 Feb;118(2):326-42. doi: 10.1111/jam.12707. Epub 2014 Dec 21.


Presence of disinfectant resistance genes in Escherichia coli isolated from retail meats in the USA.

Zou L, Meng J, McDermott PF, Wang F, Yang Q, Cao G, Hoffmann M, Zhao S.

J Antimicrob Chemother. 2014 Oct;69(10):2644-9. doi: 10.1093/jac/dku197. Epub 2014 Jun 7.


Comparative genomic analysis and virulence differences in closely related salmonella enterica serotype heidelberg isolates from humans, retail meats, and animals.

Hoffmann M, Zhao S, Pettengill J, Luo Y, Monday SR, Abbott J, Ayers SL, Cinar HN, Muruvanda T, Li C, Allard MW, Whichard J, Meng J, Brown EW, McDermott PF.

Genome Biol Evol. 2014 May;6(5):1046-68. doi: 10.1093/gbe/evu079.


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.


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.


Antimicrobial resistance in campylobacter: susceptibility testing methods and resistance trends.

Ge B, Wang F, Sjölund-Karlsson M, McDermott PF.

J Microbiol Methods. 2013 Oct;95(1):57-67. doi: 10.1016/j.mimet.2013.06.021. Epub 2013 Jul 1. Review.


Retrospective analysis of Salmonella, Campylobacter, Escherichia coli, and Enterococcus in animal feed ingredients.

Ge B, LaFon PC, Carter PJ, McDermott SD, Abbott J, Glenn A, Ayers SL, Friedman SL, Paige JC, Wagner DD, Zhao S, McDermott PF, Rasmussen MA.

Foodborne Pathog Dis. 2013 Aug;10(8):684-91. doi: 10.1089/fpd.2012.1470. Epub 2013 May 21.


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.


Antimicrobial resistance genes in multidrug-resistant Salmonella enterica isolated from animals, retail meats, and humans in the United States and Canada.

Glenn LM, Lindsey RL, Folster JP, Pecic G, Boerlin P, Gilmour MW, Harbottle H, Zhao S, McDermott PF, Fedorka-Cray PJ, Frye JG.

Microb Drug Resist. 2013 Jun;19(3):175-84. doi: 10.1089/mdr.2012.0177. Epub 2013 Jan 25.


Antimicrobial-resistant Campylobacter in the food chain in Mexico.

Zaidi MB, McDermott PF, Campos FD, Chim R, Leon M, Vazquez G, Figueroa G, Lopez E, Contreras J, Estrada-Garcia T.

Foodborne Pathog Dis. 2012 Sep;9(9):841-7. doi: 10.1089/fpd.2012.1127. Epub 2012 Aug 7.


Characterization of extended-spectrum cephalosporin-resistant Salmonella enterica serovar Heidelberg isolated from food animals, retail meat, and humans in the United States 2009.

Folster JP, Pecic G, Singh A, Duval B, Rickert R, Ayers S, Abbott J, McGlinchey B, Bauer-Turpin J, Haro J, Hise K, Zhao S, Fedorka-Cray PJ, Whichard J, McDermott PF.

Foodborne Pathog Dis. 2012 Jul;9(7):638-45. doi: 10.1089/fpd.2012.1130.


Genome sequences of five Salmonella enterica serovar Heidelberg isolates associated with a 2011 multistate outbreak in the United States.

Hoffmann M, Zhao S, Luo Y, Li C, Folster JP, Whichard J, Allard MW, Brown EW, McDermott PF.

J Bacteriol. 2012 Jun;194(12):3274-5. doi: 10.1128/JB.00419-12.


Antimicrobial drug resistance in Escherichia coli from humans and food animals, United States, 1950-2002.

Tadesse DA, Zhao S, Tong E, Ayers S, Singh A, Bartholomew MJ, McDermott PF.

Emerg Infect Dis. 2012 May;18(5):741-9. doi: 10.3201/eid1805.111153.


Comparison of the prevalences and antimicrobial resistances of Escherichia coli isolates from different retail meats in the United States, 2002 to 2008.

Zhao S, Blickenstaff K, Bodeis-Jones S, Gaines SA, Tong E, McDermott PF.

Appl Environ Microbiol. 2012 Mar;78(6):1701-7. doi: 10.1128/AEM.07522-11. Epub 2012 Jan 13.


Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution.

Fricke WF, Mammel MK, McDermott PF, Tartera C, White DG, Leclerc JE, Ravel J, Cebula TA.

J Bacteriol. 2011 Jul;193(14):3556-68. doi: 10.1128/JB.00297-11. Epub 2011 May 20.


Escherichia coli from retail meats carry genes associated with uropathogenic Escherichia coli, but are weakly invasive in human bladder cell culture.

Xia X, Meng J, McDermott PF, Zhao S.

J Appl Microbiol. 2011 May;110(5):1166-76. doi: 10.1111/j.1365-2672.2011.04978.x. Epub 2011 Mar 14.


Identification and antimicrobial resistance of extraintestinal pathogenic Escherichia coli from retail meats.

Xia X, Meng J, Zhao S, Bodeis-Jones S, Gaines SA, Ayers SL, McDermott PF.

J Food Prot. 2011 Jan;74(1):38-44. doi: 10.4315/0362-028X.JFP-10-251.


Horizontal gene transfer of a ColV plasmid has resulted in a dominant avian clonal type of Salmonella enterica serovar Kentucky.

Johnson TJ, Thorsness JL, Anderson CP, Lynne AM, Foley SL, Han J, Fricke WF, McDermott PF, White DG, Khatri M, Stell AL, Flores C, Singer RS.

PLoS One. 2010 Dec 22;5(12):e15524. doi: 10.1371/journal.pone.0015524.


Plasmid-mediated quinolone resistance among non-Typhi Salmonella enterica isolates, USA.

Sjölund-Karlsson M, Howie R, Rickert R, Krueger A, Tran TT, Zhao S, Ball T, Haro J, Pecic G, Joyce K, Fedorka-Cray PJ, Whichard JM, McDermott PF.

Emerg Infect Dis. 2010 Nov;16(11):1789-91. doi: 10.3201/eid1611.100464.


Antimicrobial resistance of Campylobacter isolates from retail meat in the United States between 2002 and 2007.

Zhao S, Young SR, Tong E, Abbott JW, Womack N, Friedman SL, McDermott PF.

Appl Environ Microbiol. 2010 Dec;76(24):7949-56. doi: 10.1128/AEM.01297-10. Epub 2010 Oct 22.


Multidrug-resistant Salmonella isolates from retail chicken meat compared with human clinical isolates.

M'ikanatha NM, Sandt CH, Localio AR, Tewari D, Rankin SC, Whichard JM, Altekruse SF, Lautenbach E, Folster JP, Russo A, Chiller TM, Reynolds SM, McDermott PF.

Foodborne Pathog Dis. 2010 Aug;7(8):929-34. doi: 10.1089/fpd.2009.0499.


Antimicrobial resistance, virulence, and genotypic profile comparison of Campylobacter jejuni and Campylobacter coli isolated from humans and retail meats.

Thakur S, Zhao S, McDermott PF, Harbottle H, Abbott J, English L, Gebreyes WA, White DG.

Foodborne Pathog Dis. 2010 Jul;7(7):835-44. doi: 10.1089/fpd.2009.0487.


Evaluation of antimicrobial resistance phenotypes for predicting multidrug-resistant Salmonella recovered from retail meats and humans in the United States.

Whichard JM, Medalla F, Hoekstra RM, McDermott PF, Joyce K, Chiller T, Barrett TJ, White DG.

J Food Prot. 2010 Mar;73(3):445-51.


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