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For: Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, Taboada EN. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PLoS One 2016;11:e0147101. [PMID: 26800248 PMCID: PMC4723315 DOI: 10.1371/journal.pone.0147101] [Citation(s) in RCA: 378] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/29/2015] [Indexed: 11/28/2022]  Open
Number Cited by Other Article(s)
301
Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Tolerance to arsenic contaminant among multidrug‐resistant and copper‐tolerant Salmonella successful clones is associated with diverse ars operons and genetic contexts. Environ Microbiol 2020;22:2829-2842. [DOI: 10.1111/1462-2920.15016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/13/2020] [Accepted: 04/08/2020] [Indexed: 11/28/2022]
302
Highly Sensitive and Specific Detection and Serotyping of Five Prevalent Salmonella Serovars by Multiple Cross-Displacement Amplification. J Mol Diagn 2020;22:708-719. [PMID: 32359725 DOI: 10.1016/j.jmoldx.2020.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 12/16/2019] [Accepted: 02/20/2020] [Indexed: 02/08/2023]  Open
303
A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium. Food Microbiol 2020;91:103534. [PMID: 32539977 DOI: 10.1016/j.fm.2020.103534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/22/2020] [Indexed: 11/23/2022]
304
Miller EA, Elnekave E, Flores-Figueroa C, Johnson A, Kearney A, Munoz-Aguayo J, Tagg KA, Tschetter L, Weber BP, Nadon CA, Boxrud D, Singer RS, Folster JP, Johnson TJ. Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America. mSphere 2020;5:e00056-20. [PMID: 32295868 PMCID: PMC7160679 DOI: 10.1128/msphere.00056-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/26/2020] [Indexed: 01/09/2023]  Open
305
Alba P, Leekitcharoenphon P, Carfora V, Amoruso R, Cordaro G, Di Matteo P, Ianzano A, Iurescia M, Diaconu EL, Study Group EEAN, Pedersen SK, Guerra B, Hendriksen RS, Franco A, Battisti A. Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid. Microb Genom 2020;6. [PMID: 32271142 PMCID: PMC7371121 DOI: 10.1099/mgen.0.000365] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
306
Cooper AL, Low AJ, Koziol AG, Thomas MC, Leclair D, Tamber S, Wong A, Blais BW, Carrillo CD. Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance. Front Microbiol 2020;11:549. [PMID: 32318038 PMCID: PMC7147080 DOI: 10.3389/fmicb.2020.00549] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/13/2020] [Indexed: 01/21/2023]  Open
307
Wu Y, Hu Q, Dehinwal R, Rakov AV, Grams N, Clemens EC, Hofmann J, Okeke IN, Schifferli DM. The Not so Good, the Bad and the Ugly: Differential Bacterial Adhesion and Invasion Mediated by Salmonella PagN Allelic Variants. Microorganisms 2020;8:microorganisms8040489. [PMID: 32235448 PMCID: PMC7232170 DOI: 10.3390/microorganisms8040489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/24/2020] [Accepted: 03/28/2020] [Indexed: 11/21/2022]  Open
308
Genome-based Salmonella serotyping as the new gold standard. Sci Rep 2020;10:4333. [PMID: 32152449 PMCID: PMC7062728 DOI: 10.1038/s41598-020-61254-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 02/25/2020] [Indexed: 11/08/2022]  Open
309
Mastrorilli E, Petrin S, Orsini M, Longo A, Cozza D, Luzzi I, Ricci A, Barco L, Losasso C. Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017. BMC Genomics 2020;21:202. [PMID: 32131727 PMCID: PMC7057659 DOI: 10.1186/s12864-020-6588-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/18/2020] [Indexed: 12/24/2022]  Open
310
Gu D, Wang Z, Tian Y, Kang X, Meng C, Chen X, Pan Z, Jiao X. Prevalence of Salmonella Isolates and Their Distribution Based on Whole-Genome Sequence in a Chicken Slaughterhouse in Jiangsu, China. Front Vet Sci 2020;7:29. [PMID: 32154275 PMCID: PMC7046563 DOI: 10.3389/fvets.2020.00029] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/14/2020] [Indexed: 11/29/2022]  Open
311
Performance and Accuracy of Four Open-Source Tools for In Silico Serotyping of Salmonella spp. Based on Whole-Genome Short-Read Sequencing Data. Appl Environ Microbiol 2020;86:AEM.02265-19. [PMID: 31862714 PMCID: PMC7028957 DOI: 10.1128/aem.02265-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022]  Open
312
Uelze L, Grützke J, Borowiak M, Hammerl JA, Juraschek K, Deneke C, Tausch SH, Malorny B. Typing methods based on whole genome sequencing data. ONE HEALTH OUTLOOK 2020;2:3. [PMID: 33829127 PMCID: PMC7993478 DOI: 10.1186/s42522-020-0010-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/08/2020] [Indexed: 05/12/2023]
313
Borowiak M, Baumann B, Fischer J, Thomas K, Deneke C, Hammerl JA, Szabo I, Malorny B. Development of a Novel mcr-6 to mcr-9 Multiplex PCR and Assessment of mcr-1 to mcr-9 Occurrence in Colistin-Resistant Salmonella enterica Isolates From Environment, Feed, Animals and Food (2011-2018) in Germany. Front Microbiol 2020;11:80. [PMID: 32117115 PMCID: PMC7011100 DOI: 10.3389/fmicb.2020.00080] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/15/2020] [Indexed: 11/15/2022]  Open
314
Kipper D, Hellfeldt RM, De Carli S, Lehmann FKM, Fonseca ASK, Ikuta N, Lunge VR. Salmonella serotype assignment by sequencing analysis of intergenic regions of ribosomal RNA operons. Poult Sci 2020;98:5989-5998. [PMID: 31134273 DOI: 10.3382/ps/pez285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/03/2019] [Indexed: 02/02/2023]  Open
315
Zhou Z, Alikhan NF, Mohamed K, Fan Y, Achtman M. The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res 2020;30:138-152. [PMID: 31809257 PMCID: PMC6961584 DOI: 10.1101/gr.251678.119] [Citation(s) in RCA: 604] [Impact Index Per Article: 120.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 12/03/2019] [Indexed: 01/08/2023]
316
Saltykova A, Mattheus W, Bertrand S, Roosens NHC, Marchal K, De Keersmaecker SCJ. Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept. Front Microbiol 2019;10:2897. [PMID: 31921072 PMCID: PMC6930190 DOI: 10.3389/fmicb.2019.02897] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/02/2019] [Indexed: 12/19/2022]  Open
317
Silveira L, Pinto M, Isidro J, Pista Â, Themudo P, Vieira L, Machado J, Gomes JP. Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal. Int J Genomics 2019;2019:1860275. [PMID: 31950026 PMCID: PMC6948285 DOI: 10.1155/2019/1860275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]  Open
318
Zuo L, Jiang M, Jiang Y, Shi X, Li Y, Lin Y, Qiu Y, Deng Y, Li M, Lin Z, Liao Y, Xie J, Li Q, Hu Q. Multiplex ligation reaction based on probe melting curve analysis: a pragmatic approach for the identification of 30 common Salmonella serovars. Ann Clin Microbiol Antimicrob 2019;18:39. [PMID: 31805936 PMCID: PMC6894471 DOI: 10.1186/s12941-019-0338-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/18/2019] [Indexed: 01/13/2023]  Open
319
Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Malorny B, Ribeiro Duarte AS, Torpdahl M, da Silva Felício MT, Guerra B, Rossi M, Herman L. Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms. EFSA J 2019;17:e05898. [PMID: 32626197 PMCID: PMC7008917 DOI: 10.2903/j.efsa.2019.5898] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
320
Kingsbury JM, Thom K, Erskine H, Olsen L, Soboleva T. Prevalence and Genetic Analysis of Salmonella enterica from a Cross-Sectional Survey of the New Zealand Egg Production Environment. J Food Prot 2019;82:2201-2214. [PMID: 31742446 DOI: 10.4315/0362-028x.jfp-19-159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
321
Chattaway MA, Dallman TJ, Larkin L, Nair S, McCormick J, Mikhail A, Hartman H, Godbole G, Powell D, Day M, Smith R, Grant K. The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales. Front Public Health 2019;7:317. [PMID: 31824904 PMCID: PMC6881236 DOI: 10.3389/fpubh.2019.00317] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/15/2019] [Indexed: 01/26/2023]  Open
322
Robertson J, Lin J, Wren-Hedgus A, Arya G, Carrillo C, Nash JHE. Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella. PLoS One 2019;14:e0218638. [PMID: 31738764 PMCID: PMC6860452 DOI: 10.1371/journal.pone.0218638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/01/2019] [Indexed: 11/29/2022]  Open
323
SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data. Appl Environ Microbiol 2019;85:AEM.01746-19. [PMID: 31540993 DOI: 10.1128/aem.01746-19] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/17/2019] [Indexed: 11/20/2022]  Open
324
Diep B, Barretto C, Portmann AC, Fournier C, Karczmarek A, Voets G, Li S, Deng X, Klijn A. Salmonella Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an in silico Platform Using Whole Genome Sequencing Data. Front Microbiol 2019;10:2554. [PMID: 31781065 PMCID: PMC6859910 DOI: 10.3389/fmicb.2019.02554] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/22/2019] [Indexed: 11/13/2022]  Open
325
Vila Nova M, Durimel K, La K, Felten A, Bessières P, Mistou MY, Mariadassou M, Radomski N. Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale. BMC Genomics 2019;20:814. [PMID: 31694533 PMCID: PMC6836353 DOI: 10.1186/s12864-019-6188-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/15/2019] [Indexed: 12/14/2022]  Open
326
Moore MM, Nucci MJ, Madson SM, Wagley GS, Keys CE, Brown EW, McQUISTON JR, Fields PI. Evaluation of a Bead-Based Salmonella Molecular Serotyping Method for Salmonella Isolated from Food and Environmental Samples. J Food Prot 2019;82:1973-1987. [PMID: 31644335 DOI: 10.4315/0362-028x.jfp-18-600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
327
Rehman MA, Hasted TL, Persaud-Lachhman MG, Yin X, Carrillo C, Diarra MS. Genome Analysis and Multiplex PCR Method for the Molecular Detection of Coresistance to Cephalosporins and Fosfomycin in Salmonella enterica Serovar Heidelberg. J Food Prot 2019;82:1938-1949. [PMID: 31633426 DOI: 10.4315/0362-028x.jfp-19-205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
328
Uelze L, Borowiak M, Deneke C, Jacobs C, Szabó I, Tausch SH, Malorny B. First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep. Gut Pathog 2019;11:48. [PMID: 31636715 PMCID: PMC6791114 DOI: 10.1186/s13099-019-0330-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/27/2019] [Indexed: 11/10/2022]  Open
329
Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning. mSystems 2019;4:4/4/e00211-19. [PMID: 31387929 PMCID: PMC6687941 DOI: 10.1128/msystems.00211-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
330
Fenske GJ, Thachil A, McDonough PL, Glaser A, Scaria J. Geography Shapes the Population Genomics of Salmonella enterica Dublin. Genome Biol Evol 2019;11:2220-2231. [PMID: 31329231 PMCID: PMC6703130 DOI: 10.1093/gbe/evz158] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 01/11/2023]  Open
331
Petronella N, Kundra P, Auclair O, Hébert K, Rao M, Kingsley K, De Bruyne K, Banerjee S, Gill A, Pagotto F, Tamber S, Ronholm J. Changes detected in the genome sequences of Escherichia coli, Listeria monocytogenes, Vibrio parahaemolyticus, and Salmonella enterica after serial subculturing. Can J Microbiol 2019;65:842-850. [PMID: 31356758 DOI: 10.1139/cjm-2019-0235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
332
Cheng RA, Wiedmann M. The ADP-Ribosylating Toxins of Salmonella. Toxins (Basel) 2019;11:E416. [PMID: 31315299 PMCID: PMC6669713 DOI: 10.3390/toxins11070416] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/22/2022]  Open
333
Tang S, Orsi RH, Luo H, Ge C, Zhang G, Baker RC, Stevenson A, Wiedmann M. Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella. Front Microbiol 2019;10:1591. [PMID: 31354679 PMCID: PMC6639432 DOI: 10.3389/fmicb.2019.01591] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/26/2019] [Indexed: 01/26/2023]  Open
334
Cheng RA, Eade CR, Wiedmann M. Embracing Diversity: Differences in Virulence Mechanisms, Disease Severity, and Host Adaptations Contribute to the Success of Nontyphoidal Salmonella as a Foodborne Pathogen. Front Microbiol 2019;10:1368. [PMID: 31316476 PMCID: PMC6611429 DOI: 10.3389/fmicb.2019.01368] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/31/2019] [Indexed: 12/19/2022]  Open
335
Wick RR, Judd LM, Holt KE. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol 2019;20:129. [PMID: 31234903 PMCID: PMC6591954 DOI: 10.1186/s13059-019-1727-y] [Citation(s) in RCA: 942] [Impact Index Per Article: 157.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/30/2019] [Indexed: 11/28/2022]  Open
336
Wick RR, Judd LM, Holt KE. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol 2019. [PMID: 31234903 DOI: 10.1186/s13059–019–1727–y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
337
Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla CMY-2 and bla SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries. Antimicrob Agents Chemother 2019;63:AAC.02546-18. [PMID: 31085509 DOI: 10.1128/aac.02546-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/01/2019] [Indexed: 11/20/2022]  Open
338
Pulford CV, Wenner N, Redway ML, Rodwell EV, Webster HJ, Escudero R, Kröger C, Canals R, Rowe W, Lopez J, Hall N, Rowley PD, Timofte D, Harrison RA, Baker KS, Hinton JCD. The diversity, evolution and ecology of Salmonella in venomous snakes. PLoS Negl Trop Dis 2019;13:e0007169. [PMID: 31163033 PMCID: PMC6548357 DOI: 10.1371/journal.pntd.0007169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022]  Open
339
Mangat CS, Bekal S, Avery BP, Côté G, Daignault D, Doualla-Bell F, Finley R, Lefebvre B, Bharat A, Parmley EJ, Reid-Smith RJ, Longtin J, Irwin RJ, Mulvey MR. Genomic Investigation of the Emergence of Invasive Multidrug-Resistant Salmonella enterica Serovar Dublin in Humans and Animals in Canada. Antimicrob Agents Chemother 2019;63:e00108-19. [PMID: 31036694 PMCID: PMC6535508 DOI: 10.1128/aac.00108-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/07/2019] [Indexed: 11/20/2022]  Open
340
Relevance of Food Microbiology Issues to Current Trends (2008-2018) in Food Production and Imported Foods. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
341
Molecular Source Tracking and Molecular Subtyping. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
342
Rakov AV, Mastriani E, Liu SL, Schifferli DM. Association of Salmonella virulence factor alleles with intestinal and invasive serovars. BMC Genomics 2019;20:429. [PMID: 31138114 PMCID: PMC6540521 DOI: 10.1186/s12864-019-5809-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/20/2019] [Indexed: 12/12/2022]  Open
343
Collineau L, Boerlin P, Carson CA, Chapman B, Fazil A, Hetman B, McEwen SA, Parmley EJ, Reid-Smith RJ, Taboada EN, Smith BA. Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges. Front Microbiol 2019;10:1107. [PMID: 31231317 PMCID: PMC6558386 DOI: 10.3389/fmicb.2019.01107] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/01/2019] [Indexed: 12/20/2022]  Open
344
Ceric O, Tyson GH, Goodman LB, Mitchell PK, Zhang Y, Prarat M, Cui J, Peak L, Scaria J, Antony L, Thomas M, Nemser SM, Anderson R, Thachil AJ, Franklin-Guild RJ, Slavic D, Bommineni YR, Mohan S, Sanchez S, Wilkes R, Sahin O, Hendrix GK, Lubbers B, Reed D, Jenkins T, Roy A, Paulsen D, Mani R, Olsen K, Pace L, Pulido M, Jacob M, Webb BT, Dasgupta S, Patil A, Ramachandran A, Tewari D, Thirumalapura N, Kelly DJ, Rankin SC, Lawhon SD, Wu J, Burbick CR, Reimschuessel R. Enhancing the one health initiative by using whole genome sequencing to monitor antimicrobial resistance of animal pathogens: Vet-LIRN collaborative project with veterinary diagnostic laboratories in United States and Canada. BMC Vet Res 2019;15:130. [PMID: 31060608 PMCID: PMC6501310 DOI: 10.1186/s12917-019-1864-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/05/2019] [Indexed: 01/16/2023]  Open
345
Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates. Appl Environ Microbiol 2019;85:AEM.00139-19. [PMID: 30902850 DOI: 10.1128/aem.00139-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/07/2019] [Indexed: 12/17/2022]  Open
346
Mintzer V, Moran-Gilad J, Simon-Tuval T. Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review. Clin Microbiol Infect 2019;25:1086-1095. [PMID: 31039443 DOI: 10.1016/j.cmi.2019.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022]
347
Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Gallinarum Strains Isolated from Layer Breeder Flocks in an Outbreak of Fowl Typhoid in Colombia. Microbiol Resour Announc 2019;8:8/17/e00122-19. [PMID: 31023811 PMCID: PMC6486240 DOI: 10.1128/mra.00122-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]  Open
348
Zhang X, Payne M, Lan R. In silico Identification of Serovar-Specific Genes for Salmonella Serotyping. Front Microbiol 2019;10:835. [PMID: 31068916 PMCID: PMC6491675 DOI: 10.3389/fmicb.2019.00835] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/01/2019] [Indexed: 11/23/2022]  Open
349
Loss and Gain in the Evolution of the Salmonella enterica Serovar Gallinarum Biovar Pullorum Genome. mSphere 2019;4:4/2/e00627-18. [PMID: 30944215 PMCID: PMC6449608 DOI: 10.1128/msphere.00627-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
350
Circulation of Plasmids Harboring Resistance Genes to Quinolones and/or Extended-Spectrum Cephalosporins in Multiple Salmonella enterica Serotypes from Swine in the United States. Antimicrob Agents Chemother 2019;63:AAC.02602-18. [PMID: 30745386 DOI: 10.1128/aac.02602-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/30/2019] [Indexed: 11/20/2022]  Open
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