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Closing Clostridium botulinum Group I Genomes Using a Combination of Short- and Long-Reads.

Gonzalez-Escalona N, Sharma SK.

Front Microbiol. 2020 Feb 19;11:239. doi: 10.3389/fmicb.2020.00239. eCollection 2020.


mcr-Colistin Resistance Genes Mobilized by IncX4, IncHI2, and IncI2 Plasmids in Escherichia coli of Pigs and White Stork in Spain.

Migura-Garcia L, González-López JJ, Martinez-Urtaza J, Aguirre Sánchez JR, Moreno-Mingorance A, Perez de Rozas A, Höfle U, Ramiro Y, Gonzalez-Escalona N.

Front Microbiol. 2020 Jan 17;10:3072. doi: 10.3389/fmicb.2019.03072. eCollection 2019.


Genome Sequences of Brevundimonas naejangsanensis Strain FS1091 and Bacillus amyloliquefaciens Strain FS1092, Isolated from a Fresh-Cut-Produce-Processing Plant.

Gu G, Gonzalez-Escalona N, Zheng J, Bolten S, Luo Y, Mafiz AI, Leon MS, Nou X.

Microbiol Resour Announc. 2020 Jan 23;9(4). pii: e01448-19. doi: 10.1128/MRA.01448-19.


Global Expansion of Pacific Northwest Vibrio parahaemolyticus Sequence Type 36.

Abanto M, Gavilan RG, Baker-Austin C, Gonzalez-Escalona N, Martinez-Urtaza J.

Emerg Infect Dis. 2020 Feb;26(2):323-326. doi: 10.3201/eid2602.190362.


Complete Genome Sequences of Four Salmonella enterica Strains Associated with Pistachios Assembled Using a Combination of Short- and Long-Read Sequencing.

Haendiges J, Gonzalez-Escalona N, Miller JD, Hoffmann M.

Microbiol Resour Announc. 2019 Sep 19;8(38). pii: e00975-19. doi: 10.1128/MRA.00975-19.


Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli.

González-Escalona N, Allard MA, Brown EW, Sharma S, Hoffmann M.

PLoS One. 2019 Jul 30;14(7):e0220494. doi: 10.1371/journal.pone.0220494. eCollection 2019.


Closed Genome Sequences of Three Salmonella enterica Strains Belonging to Serovars Saintpaul, Weltevreden, and Thompson, Isolated from Mexico.

Gonzalez-Escalona N, Aguirre-Sánchez JR, Ibarra-Rodríguez JR, Chaidez-Quiroz C, Martinez-Urtaza J.

Microbiol Resour Announc. 2019 Jul 11;8(28). pii: e00656-19. doi: 10.1128/MRA.00656-19.


Genomic features of colistin resistant Escherichia coli ST69 strain harboring mcr-1 on IncHI2 plasmid from raw milk cheese in Egypt.

Hammad AM, Hoffmann M, Gonzalez-Escalona N, Abbas NH, Yao K, Koenig S, Allué-Guardia A, Eppinger M.

Infect Genet Evol. 2019 Sep;73:126-131. doi: 10.1016/j.meegid.2019.04.021. Epub 2019 Apr 25.


Detection of colistin resistance mcr-1 gene in Salmonella enterica serovar Rissen isolated from mussels, Spain, 2012- to 2016.

Lozano-Leon A, Garcia-Omil C, Dalama J, Rodriguez-Souto R, Martinez-Urtaza J, Gonzalez-Escalona N.

Euro Surveill. 2019 Apr;24(16). doi: 10.2807/1560-7917.ES.2019.24.16.1900200.


Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017.

González-Escalona N, Kase JA.

PLoS One. 2019 Apr 1;14(4):e0214620. doi: 10.1371/journal.pone.0214620. eCollection 2019.


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.


Closed Genome Sequence of Salmonella enterica Serovar Richmond Strain CFSAN000191, Obtained with Nanopore Sequencing.

González-Escalona N, Yao K, Hoffmann M.

Microbiol Resour Announc. 2018 Dec 13;7(23). pii: e01472-18. doi: 10.1128/MRA.01472-18. eCollection 2018 Dec.


Closed Genome Sequences of Two Clostridium botulinum Strains Obtained by Nanopore Sequencing.

Gonzalez-Escalona N, Haendiges J, Miller JD, Sharma SK.

Microbiol Resour Announc. 2018 Sep 6;7(9). pii: e01075-18. doi: 10.1128/MRA.01075-18. eCollection 2018 Sep.


Epidemic Dynamics of Vibrio parahaemolyticus Illness in a Hotspot of Disease Emergence, Galicia, Spain.

Martinez-Urtaza J, Trinanes J, Abanto M, Lozano-Leon A, Llovo-Taboada J, Garcia-Campello M, Pousa A, Powell A, Baker-Austin C, Gonzalez-Escalona N.

Emerg Infect Dis. 2018 May;24(5):852-859. doi: 10.3201/eid2405.171700.


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.


Genomic Variation and Evolution of Vibrio parahaemolyticus ST36 over the Course of a Transcontinental Epidemic Expansion.

Martinez-Urtaza J, van Aerle R, Abanto M, Haendiges J, Myers RA, Trinanes J, Baker-Austin C, Gonzalez-Escalona N.

mBio. 2017 Nov 14;8(6). pii: e01425-17. doi: 10.1128/mBio.01425-17.


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.


Parallel Evolution of Two Clades of an Atlantic-Endemic Pathogenic Lineage of Vibrio parahaemolyticus by Independent Acquisition of Related Pathogenicity Islands.

Xu F, Gonzalez-Escalona N, Drees KP, Sebra RP, Cooper VS, Jones SH, Whistler CA.

Appl Environ Microbiol. 2017 Aug 31;83(18). pii: e01168-17. doi: 10.1128/AEM.01168-17. Print 2017 Sep 15.


Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus.

Gonzalez-Escalona N, Jolley KA, Reed E, Martinez-Urtaza J.

J Clin Microbiol. 2017 Jun;55(6):1682-1697. doi: 10.1128/JCM.00227-17. Epub 2017 Mar 22.


Sequence Type 631 Vibrio parahaemolyticus, an Emerging Foodborne Pathogen in North America.

Xu F, Gonzalez-Escalona N, Haendiges J, Myers RA, Ferguson J, Stiles T, Hickey E, Moore M, Hickey JM, Schillaci C, Mank L, DeRosia-Banick K, Matluk N, Robbins A, Sebra RP, Cooper VS, Jones SH, Whistler CA.

J Clin Microbiol. 2017 Feb;55(2):645-648. doi: 10.1128/JCM.02162-16. Epub 2016 Dec 14. No abstract available.


Non-Cholera Vibrios: The Microbial Barometer of Climate Change.

Baker-Austin C, Trinanes J, Gonzalez-Escalona N, Martinez-Urtaza J.

Trends Microbiol. 2017 Jan;25(1):76-84. doi: 10.1016/j.tim.2016.09.008. Epub 2016 Nov 12. Review.


Complete Genome Sequences of Four Enterohemolysin-Positive (ehxA) Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains.

Lorenz SC, Kotewicz ML, Hoffmann M, Gonzalez-Escalona N, Fischer M, Kase JA.

Genome Announc. 2016 Sep 1;4(5). pii: e00846-16. doi: 10.1128/genomeA.00846-16.


Is El Niño a long-distance corridor for waterborne disease?

Martinez-Urtaza J, Trinanes J, Gonzalez-Escalona N, Baker-Austin C.

Nat Microbiol. 2016 Feb 24;1:16018. doi: 10.1038/nmicrobiol.2016.18. No abstract available.


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.


Whole-Genome Sequencing Analysis of Salmonella enterica Serovar Enteritidis Isolates in Chile Provides Insights into Possible Transmission between Gulls, Poultry, and Humans.

Toro M, Retamal P, Ayers S, Barreto M, Allard M, Brown EW, Gonzalez-Escalona N.

Appl Environ Microbiol. 2016 Sep 30;82(20):6223-6232. Print 2016 Oct 15.


Outbreak of Vibrio parahaemolyticus Sequence Type 120, Peru, 2009.

Gonzalez-Escalona N, Gavilan RG, Toro M, Zamudio ML, Martinez-Urtaza J.

Emerg Infect Dis. 2016 Jul;22(7):1235-7. doi: 10.3201/eid2207.151896.


Virulence Gene Profiles and Clonal Relationships of Escherichia coli O26:H11 Isolates from Feedlot Cattle as Determined by Whole-Genome Sequencing.

Gonzalez-Escalona N, Toro M, Rump LV, Cao G, Nagaraja TG, Meng J.

Appl Environ Microbiol. 2016 Jun 13;82(13):3900-3912. doi: 10.1128/AEM.00498-16. Print 2016 Jul 1.


A Nonautochthonous U.S. Strain of Vibrio parahaemolyticus Isolated from Chesapeake Bay Oysters Caused the Outbreak in Maryland in 2010.

Haendiges J, Jones J, Myers RA, Mitchell CS, Butler E, Toro M, Gonzalez-Escalona N.

Appl Environ Microbiol. 2016 May 16;82(11):3208-3216. doi: 10.1128/AEM.00096-16. Print 2016 Jun 1.


Draft Genome Sequences of Four Xanthomonas arboricola pv. juglandis Strains Associated with Walnut Blight in Chile.

Higuera G, González-Escalona N, Véliz C, Vera F, Romero J.

Genome Announc. 2015 Oct 8;3(5). pii: e01160-15. doi: 10.1128/genomeA.01160-15.


Genome Sequences of 64 Non-O157:H7 Shiga Toxin-Producing Escherichia coli Strains.

Toro M, Cao G, Rump L, Nagaraja TG, Meng J, Gonzalez-Escalona N.

Genome Announc. 2015 Oct 1;3(5). pii: e01067-15. doi: 10.1128/genomeA.01067-15.


Simultaneous Presence of Insertion Sequence Excision Enhancer and Insertion Sequence IS629 Correlates with Increased Diversity and Virulence in Shiga Toxin-Producing Escherichia coli.

Toro M, Rump LV, Cao G, Meng J, Brown EW, Gonzalez-Escalona N.

J Clin Microbiol. 2015 Nov;53(11):3466-73. doi: 10.1128/JCM.01349-15. Epub 2015 Aug 19.


Examination of clinical and environmental Vibrio parahaemolyticus isolates by multi-locus sequence typing (MLST) and multiple-locus variable-number tandem-repeat analysis (MLVA).

Lüdeke CH, Gonzalez-Escalona N, Fischer M, Jones JL.

Front Microbiol. 2015 Jun 10;6:564. doi: 10.3389/fmicb.2015.00564. eCollection 2015.


Tracing Origins of the Salmonella Bareilly Strain Causing a Food-borne Outbreak in the United States.

Hoffmann M, Luo Y, Monday SR, Gonzalez-Escalona N, Ottesen AR, Muruvanda T, Wang C, Kastanis G, Keys C, Janies D, Senturk IF, Catalyurek UV, Wang H, Hammack TS, Wolfgang WJ, Schoonmaker-Bopp D, Chu A, Myers R, Haendiges J, Evans PS, Meng J, Strain EA, Allard MW, Brown EW.

J Infect Dis. 2016 Feb 15;213(4):502-8. doi: 10.1093/infdis/jiv297. Epub 2015 May 20.


Draft Genome Sequences of 33 Salmonella enterica Clinical and Wildlife Isolates from Chile.

Toro M, Retamal P, Allard M, Brown EW, Evans P, Gonzalez-Escalona N.

Genome Announc. 2015 Mar 19;3(2). pii: e00054-15. doi: 10.1128/genomeA.00054-15.


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.


Transoceanic spreading of pathogenic strains of Vibrio parahaemolyticus with distinctive genetic signatures in the recA gene.

González-Escalona N, Gavilan RG, Brown EW, Martinez-Urtaza J.

PLoS One. 2015 Feb 13;10(2):e0117485. doi: 10.1371/journal.pone.0117485. eCollection 2015.


Draft Genome Sequence of Bivalent Clostridium botulinum Strain IBCA10-7060, Encoding Botulinum Neurotoxin B and a New FA Mosaic Type.

Gonzalez-Escalona N, Thirunavukkarasu N, Singh A, Toro M, Brown EW, Zink D, Rummel A, Sharma SK.

Genome Announc. 2014 Dec 11;2(6). pii: e01275-14. doi: 10.1128/genomeA.01275-14.


Evaluation and comparison of rapid methods for the detection of Salmonella in naturally contaminated pine nuts using different pre enrichment media.

Wang H, Gill VS, Cheng CM, Gonzalez-Escalona N, Irvin KA, Zheng J, Bell RL, Jacobson AP, Hammack TS.

Food Microbiol. 2015 Apr;46:58-65. doi: 10.1016/ Epub 2014 Jul 22.


Genomic diversity and virulence profiles of historical Escherichia coli O157 strains isolated from clinical and environmental sources.

Rump LV, Gonzalez-Escalona N, Ju W, Wang F, Cao G, Meng S, Meng J.

Appl Environ Microbiol. 2015 Jan;81(2):569-77. doi: 10.1128/AEM.02616-14. Epub 2014 Nov 7.


An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella.

Pettengill JB, Luo Y, Davis S, Chen Y, Gonzalez-Escalona N, Ottesen A, Rand H, Allard MW, Strain E.

PeerJ. 2014 Oct 14;2:e620. doi: 10.7717/peerj.620. eCollection 2014.


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.


Pandemic Vibrio parahaemolyticus, Maryland, USA, 2012.

Haendiges J, Rock M, Myers RA, Brown EW, Evans P, Gonzalez-Escalona N.

Emerg Infect Dis. 2014 Apr;20(4):718-20. doi: 10.3201/eid2004.130818. No abstract available.


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.


Genetic characterization of trh positive Vibrio spp. isolated from Norway.

Ellingsen AB, Olsen JS, Granum PE, Rørvik LM, González-Escalona N.

Front Cell Infect Microbiol. 2013 Dec 25;3:107. doi: 10.3389/fcimb.2013.00107. eCollection 2013.


Draft Genome Sequences of Two Salmonella Strains from the SARA Collection, SARA64 (Muenchen) and SARA33 (Heidelberg), Provide Insight into Their Antibiotic Resistance.

Kroft BS, Brown EW, Meng J, Gonzalez-Escalona N.

Genome Announc. 2013 Oct 3;1(5). pii: e00806-13. doi: 10.1128/genomeA.00806-13.


Draft Genome Sequences of Two O104:H21 Escherichia coli Isolates Causing Hemorrhagic Colitis during a 1994 Montana Outbreak Provide Insight into Their Pathogenicity.

Gonzalez-Escalona N, McFarland MA, Rump LV, Payne J, Andrzejewski D, Brown EW, Evans PS, Croley TR.

Genome Announc. 2013 Oct 3;1(5). pii: e00805-13. doi: 10.1128/genomeA.00805-13.


Salmonella enterica diversity in central Californian coastal waterways.

Walters SP, González-Escalona N, Son I, Melka DC, Sassoubre LM, Boehm AB.

Appl Environ Microbiol. 2013 Jul;79(14):4199-209. doi: 10.1128/AEM.00930-13. Epub 2013 Apr 26.


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.


Population structure of clinical and environmental Vibrio parahaemolyticus from the Pacific Northwest coast of the United States.

Turner JW, Paranjpye RN, Landis ED, Biryukov SV, González-Escalona N, Nilsson WB, Strom MS.

PLoS One. 2013;8(2):e55726. doi: 10.1371/journal.pone.0055726. Epub 2013 Feb 7.

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