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SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment. Microbiome. 2021 06 08; 9(1):132.
Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM. PMID: 34103074.
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HumansPHPublic Health
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Enteric Viruses and Pepper Mild Mottle Virus Show Significant Correlation in Select Mid-Atlantic Agricultural Waters. Appl Environ Microbiol. 2021 Apr 23.
Anderson-Coughlin BL, Craighead S, Kelly A, Gartley S, Vanore A, Johnson G, Jiang C, Haymaker J, White C, Foust D, Duncan R, East C, Handy ET, Bradshaw R, Murray R, Kulkarni P, Callahan MT, Solaiman S, Betancourt W, Gerba C, Allard S, Parveen S, Hashem F, Micallef SA, Sapkota A, Sapkota AR, Sharma M, Kniel KE. PMID: 33893119.
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Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome. 2021 01 22; 9(1):25.
Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 33482920.
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3 Fields:
Translation:
Humans
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Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment. medRxiv. 2020 Nov 22.
Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrel K, Jiang L, Martino C, Diner R, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia M, Chiang L, Salido RA, Shaffer JP, Bryant M, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vazquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney D, Allard SM. PMID: 33236030.
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Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond. Environ Microbiome. 2020 Oct 28; 15(1):18.
Chopyk J, Nasko DJ, Allard S, Bui A, Pop M, Mongodin EF, Sapkota AR. PMID: 33902740.
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Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems. mSystems. 2020 Oct 20; 5(5).
Allard SM, Costa MT, Bulseco AN, Helfer V, Wilkins LGE, Hassenrück C, Zengler K, Zimmer M, Erazo N, Mazza Rodrigues JL, Duke N, Melo VMM, Vanwonterghem I, Junca H, Makonde HM, Jiménez DJ, Tavares TCL, Fusi M, Daffonchio D, Duarte CM, Peixoto RS, Rosado AS, Gilbert JA, Bowman J. PMID: 33082281.
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Impact of high precipitation and temperature events on the distribution of emerging contaminants in surface water in the Mid-Atlantic, United States. Sci Total Environ. 2021 Feb 10; 755(Pt 2):142552.
Zhu L, Jiang C, Panthi S, Allard SM, Sapkota AR, Sapkota A. PMID: 33059138.
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Longitudinal Assessment of the Dynamics of Escherichia coli, Total Coliforms, Enterococcus spp., and Aeromonas spp. in Alternative Irrigation Water Sources: a CONSERVE Study. Appl Environ Microbiol. 2020 10 01; 86(20).
Solaiman S, Allard SM, Callahan MT, Jiang C, Handy E, East C, Haymaker J, Bui A, Craddock H, Murray R, Kulkarni P, Anderson-Coughlin B, Craighead S, Gartley S, Vanore A, Duncan R, Foust D, Taabodi M, Sapkota A, May E, Hashem F, Parveen S, Kniel K, Sharma M, Sapkota AR, Micallef SA. PMID: 32769196.
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PubMed Mentions:
2 Fields:
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CellsPHPublic Health
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Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Res Sq. 2020 Aug 18.
Minich J, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32839765.
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Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs. medRxiv. 2020 May 18.
Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert JA, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32511552.
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Prevalence of Salmonella and Listeria monocytogenes in non-traditional irrigation waters in the Mid-Atlantic United States is affected by water type, season, and recovery method. PLoS One. 2020; 15(3):e0229365.
Sharma M, Handy ET, East CL, Kim S, Jiang C, Callahan MT, Allard SM, Micallef S, Craighead S, Anderson-Coughlin B, Gartley S, Vanore A, Kniel KE, Haymaker J, Duncan R, Foust D, White C, Taabodi M, Hashem F, Parveen S, May E, Bui A, Craddock H, Kulkarni P, Murray RT, Sapkota AR. PMID: 32182252.
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PubMed Mentions:
8 Fields:
Translation:
CellsPHPublic Health
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Rain induces temporary shifts in epiphytic bacterial communities of cucumber and tomato fruit. Sci Rep. 2020 02 04; 10(1):1765.
Allard SM, Ottesen AR, Micallef SA. PMID: 32020033.
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3 Fields:
Translation:
AnimalsCellsPHPublic Health
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Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics. Sci Total Environ. 2020 Mar 01; 706:135395.
Chopyk J, Nasko DJ, Allard S, Callahan MT, Bui A, Ferelli AMC, Chattopadhyay S, Mongodin EF, Pop M, Micallef SA, Sapkota AR. PMID: 31846873.
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PubMed Mentions:
1 Fields:
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CellsPHPublic Health
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Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications. Water Res. 2020 Feb 01; 169:115250.
Chopyk J, Nasko DJ, Allard S, Bui A, Treangen T, Pop M, Mongodin EF, Sapkota AR. PMID: 31726395.
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3 Fields:
Translation:
HumansPHPublic Health
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Pharmaceuticals, herbicides, and disinfectants in agricultural water sources. Environ Res. 2019 07; 174:1-8.
Panthi S, Sapkota AR, Raspanti G, Allard SM, Bui A, Craddock HA, Murray R, Zhu L, East C, Handy E, Callahan MT, Haymaker J, Kulkarni P, Anderson B, Craighead S, Gartley S, Vanore A, Betancourt WQ, Duncan R, Foust D, Sharma M, Micallef SA, Gerba C, Parveen S, Hashem F, May E, Kniel K, Pop M, Ravishankar S, Sapkota A. PMID: 31015109.
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1 Fields:
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PHPublic Health
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Quenching by sodium thiosulfate does not influence 16S rRNA gene sequencing profiles of reclaimed water from three sites in the Mid-Atlantic, United States. Environ Res. 2019 05; 172:296-300.
Allard SM, Solaiman S, Callahan MT, Bui A, Craddock H, Haymaker J, Foust D, Duncan R, Smyth E, Mongodin EF, Hashem F, May E, Micallef SA, Sapkota AR. PMID: 30822563.
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PHPublic Health
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Prevalence of Shiga-toxigenic and atypical enteropathogenic Escherichia coli in untreated surface water and reclaimed water in the Mid-Atlantic U.S. Environ Res. 2019 05; 172:630-636.
Haymaker J, Sharma M, Parveen S, Hashem F, May EB, Handy ET, White C, East C, Bradshaw R, Micallef SA, Callahan MT, Allard S, Anderson B, Craighead S, Gartley S, Vanore A, Kniel KE, Solaiman S, Bui A, Murray R, Craddock HA, Kulkarni P, Foust D, Duncan R, Taabodi M, Sapkota AR. PMID: 30878734.
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PubMed Mentions:
5 Fields:
Translation:
CellsPHPublic Health
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Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops. Sci Total Environ. 2019 May 20; 666:461-471.
Allard SM, Callahan MT, Bui A, Ferelli AMC, Chopyk J, Chattopadhyay S, Mongodin EF, Micallef SA, Sapkota AR. PMID: 30802661.
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PubMed Mentions:
5 Fields:
Translation:
AnimalsCellsPHPublic Health
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Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. Microbiome. 2018 11 05; 6(1):197.
Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ. PMID: 30396371.
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2 Fields:
Translation:
Humans
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Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations. Front Microbiol. 2018; 9:792.
Chopyk J, Allard S, Nasko DJ, Bui A, Mongodin EF, Sapkota AR. PMID: 29740420.
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Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers. Sci Total Environ. 2016 Dec 15; 573:555-563.
Allard SM, Walsh CS, Wallis AE, Ottesen AR, Brown EW, Micallef SA. PMID: 27580466.
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PubMed Mentions:
8 Fields:
Translation:
AnimalsPHPublic Health
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Ecological prevalence, genetic diversity, and epidemiological aspects of Salmonella isolated from tomato agricultural regions of the Virginia Eastern Shore. Front Microbiol. 2015; 6:415.
Bell RL, Zheng J, Burrows E, Allard S, Wang CY, Keys CE, Melka DC, Strain E, Luo Y, Allard MW, Rideout S, Brown EW. PMID: 25999938.
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In situ evaluation of Paenibacillus alvei in reducing carriage of Salmonella enterica serovar Newport on whole tomato plants. Appl Environ Microbiol. 2014 Jul; 80(13):3842-9.
Allard S, Enurah A, Strain E, Millner P, Rideout SL, Brown EW, Zheng J. PMID: 24747888.
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PubMed Mentions:
16 Fields:
Translation:
AnimalsCellsPHPublic Health
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Draft Genome Sequences of Paenibacillus alvei A6-6i and TS-15. Genome Announc. 2013 Aug 29; 1(5).
Luo Y, Wang C, Allard S, Strain E, Allard MW, Brown EW, Zheng J. PMID: 23990585.
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Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol. 2013 May 24; 13:114.
Ottesen AR, González Peña A, White JR, Pettengill JB, Li C, Allard S, Rideout S, Allard M, Hill T, Evans P, Strain E, Musser S, Knight R, Brown E. PMID: 23705801.
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PubMed Mentions:
57 Fields:
Translation:
AnimalsCells
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Colonization and internalization of Salmonella enterica in tomato plants. Appl Environ Microbiol. 2013 Apr; 79(8):2494-502.
Zheng J, Allard S, Reynolds S, Millner P, Arce G, Blodgett RJ, Brown EW. PMID: 23377940.
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PubMed Mentions:
23 Fields:
Translation:
HumansAnimalsCellsPHPublic Health