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For: Judge K, Harris SR, Reuter S, Parkhill J, Peacock SJ. Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes. J Antimicrob Chemother 2015;70:2775-8. [PMID: 26221019 PMCID: PMC4566964 DOI: 10.1093/jac/dkv206] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/09/2015] [Accepted: 06/17/2015] [Indexed: 01/13/2023]  Open
Number Cited by Other Article(s)
1
Frias-De-Diego A, Jara M, Lanzas C. Influence of Sequencing Technology on Pangenome-Level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens. Open Forum Infect Dis 2025;12:ofaf183. [PMID: 40212029 PMCID: PMC11983279 DOI: 10.1093/ofid/ofaf183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2025] [Accepted: 03/24/2025] [Indexed: 04/13/2025]  Open
2
Gu W, Wang J, Qin X, Duan M, Wang M, Guan Y, Xu X. The performance of nanopore sequencing in rapid detection of pathogens and antimicrobial resistance genes in blood cultures. Diagn Microbiol Infect Dis 2025;111:116720. [PMID: 39899948 DOI: 10.1016/j.diagmicrobio.2025.116720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 01/07/2025] [Accepted: 01/28/2025] [Indexed: 02/05/2025]
3
Frias-De-Diego A, Jara M, Lanzas C. Influence of Sequencing Technology on Pangenome-level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.08.631980. [PMID: 39829834 PMCID: PMC11741274 DOI: 10.1101/2025.01.08.631980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
4
Hikida H, Okazaki Y, Zhang R, Nguyen TT, Ogata H. A rapid genome-wide analysis of isolated giant viruses using MinION sequencing. Environ Microbiol 2023;25:2621-2635. [PMID: 37543720 DOI: 10.1111/1462-2920.16476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/20/2023] [Indexed: 08/07/2023]
5
Yamin D, Uskoković V, Wakil AM, Goni MD, Shamsuddin SH, Mustafa FH, Alfouzan WA, Alissa M, Alshengeti A, Almaghrabi RH, Fares MAA, Garout M, Al Kaabi NA, Alshehri AA, Ali HM, Rabaan AA, Aldubisi FA, Yean CY, Yusof NY. Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria. Diagnostics (Basel) 2023;13:3246. [PMID: 37892067 PMCID: PMC10606640 DOI: 10.3390/diagnostics13203246] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023]  Open
6
Ju Y, Pu M, Sun K, Song G, Geng J. Nanopore Electrochemistry for Pathogen Detection. Chem Asian J 2022;17:e202200774. [PMID: 36069587 DOI: 10.1002/asia.202200774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Indexed: 11/05/2022]
7
Dai D, Brown C, Bürgmann H, Larsson DGJ, Nambi I, Zhang T, Flach CF, Pruden A, Vikesland PJ. Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge. MICROBIOME 2022;10:20. [PMID: 35093160 PMCID: PMC8801152 DOI: 10.1186/s40168-021-01216-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 05/10/2023]
8
Ben Khedher M, Ghedira K, Rolain JM, Ruimy R, Croce O. Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies. Int J Mol Sci 2022;23:1395. [PMID: 35163319 PMCID: PMC8835973 DOI: 10.3390/ijms23031395] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023]  Open
9
Jahan NA, Lindsey LL, Kipp EJ, Reinschmidt A, Heins BJ, Runck AM, Larsen PA. Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents. Pathogens 2021;10:pathogens10091183. [PMID: 34578215 PMCID: PMC8471018 DOI: 10.3390/pathogens10091183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 12/26/2022]  Open
10
Chan AP, Choi Y, Clarke TH, Brinkac LM, White RC, Jacobs MR, Bonomo RA, Adams MD, Fouts DE. AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates. J Antimicrob Chemother 2021;75:2760-2768. [PMID: 32681170 PMCID: PMC7556812 DOI: 10.1093/jac/dkaa266] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 05/01/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022]  Open
11
Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021;194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
12
Indelli PF, Ghirardelli S, Violante B, Amanatullah DF. Next generation sequencing for pathogen detection in periprosthetic joint infections. EFORT Open Rev 2021;6:236-244. [PMID: 34040801 PMCID: PMC8142595 DOI: 10.1302/2058-5241.6.200099] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]  Open
13
Kaprou GD, Bergšpica I, Alexa EA, Alvarez-Ordóñez A, Prieto M. Rapid Methods for Antimicrobial Resistance Diagnostics. Antibiotics (Basel) 2021;10:209. [PMID: 33672677 PMCID: PMC7924329 DOI: 10.3390/antibiotics10020209] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 02/06/2023]  Open
14
The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update. Infect Dis Clin North Am 2020;34:659-676. [PMID: 33011047 DOI: 10.1016/j.idc.2020.08.001] [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] [Indexed: 01/28/2023]
15
Cervantes J, Yokobori N, Hong BY. Genetic Identification and Drug-Resistance Characterization of Mycobacterium tuberculosis Using a Portable Sequencing Device. A Pilot Study. Antibiotics (Basel) 2020;9:antibiotics9090548. [PMID: 32867304 PMCID: PMC7559383 DOI: 10.3390/antibiotics9090548] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/18/2022]  Open
16
Adkar-Purushothama CR, Perreault JP. Impact of Nucleic Acid Sequencing on Viroid Biology. Int J Mol Sci 2020;21:ijms21155532. [PMID: 32752288 PMCID: PMC7432327 DOI: 10.3390/ijms21155532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022]  Open
17
Determining antimicrobial resistance profiles and identifying novel mutations of Neisseria gonorrhoeae genomes obtained by multiplexed MinION sequencing. SCIENCE CHINA. LIFE SCIENCES 2020;63:1063-1070. [PMID: 31784935 DOI: 10.1007/s11427-019-1558-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/25/2019] [Indexed: 01/19/2023]
18
Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system. Sci Rep 2020;10:8984. [PMID: 32488198 PMCID: PMC7265280 DOI: 10.1038/s41598-020-65740-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 05/07/2020] [Indexed: 12/18/2022]  Open
19
Comparison of High-Throughput Sequencing for Phage Display Peptide Screening on Two Commercially Available Platforms. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09858-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
20
Vasudevan K, Devanga Ragupathi NK, Jacob JJ, Veeraraghavan B. Highly accurate-single chromosomal complete genomes using IonTorrent and MinION sequencing of clinical pathogens. Genomics 2020;112:545-551. [DOI: 10.1016/j.ygeno.2019.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/13/2019] [Accepted: 04/09/2019] [Indexed: 10/27/2022]
21
Petersen LM, Martin IW, Moschetti WE, Kershaw CM, Tsongalis GJ. Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing. J Clin Microbiol 2019;58:e01315-19. [PMID: 31619531 PMCID: PMC6935936 DOI: 10.1128/jcm.01315-19] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
22
Sevim V, Lee J, Egan R, Clum A, Hundley H, Lee J, Everroad RC, Detweiler AM, Bebout BM, Pett-Ridge J, Göker M, Murray AE, Lindemann SR, Klenk HP, O'Malley R, Zane M, Cheng JF, Copeland A, Daum C, Singer E, Woyke T. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. Sci Data 2019;6:285. [PMID: 31772173 PMCID: PMC6879543 DOI: 10.1038/s41597-019-0287-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 10/31/2019] [Indexed: 11/17/2022]  Open
23
LaPierre N, Egan R, Wang W, Wang Z. De novo Nanopore read quality improvement using deep learning. BMC Bioinformatics 2019;20:552. [PMID: 31694525 PMCID: PMC6833143 DOI: 10.1186/s12859-019-3103-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/20/2019] [Indexed: 11/23/2022]  Open
24
Midha MK, Wu M, Chiu KP. Long-read sequencing in deciphering human genetics to a greater depth. Hum Genet 2019;138:1201-1215. [PMID: 31538236 DOI: 10.1007/s00439-019-02064-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
25
González-Escalona N, Allard MA, Brown EW, Sharma S, Hoffmann M. Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli. PLoS One 2019;14:e0220494. [PMID: 31361781 PMCID: PMC6667211 DOI: 10.1371/journal.pone.0220494] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/17/2019] [Indexed: 02/02/2023]  Open
26
Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med 2019;11:45. [PMID: 31345251 PMCID: PMC6657377 DOI: 10.1186/s13073-019-0660-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]  Open
27
Sheahan T, Hakstol R, Kailasam S, Glaister GD, Hudson AJ, Wieden HJ. Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing. PLoS One 2019;14:e0219961. [PMID: 31339905 PMCID: PMC6655686 DOI: 10.1371/journal.pone.0219961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/06/2019] [Indexed: 12/11/2022]  Open
28
Magi A, Semeraro R, Mingrino A, Giusti B, D'Aurizio R. Nanopore sequencing data analysis: state of the art, applications and challenges. Brief Bioinform 2019. [PMID: 28637243 DOI: 10.1093/bib/bbx062] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
29
Arango-Argoty GA, Dai D, Pruden A, Vikesland P, Heath LS, Zhang L. NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes. MICROBIOME 2019;7:88. [PMID: 31174603 PMCID: PMC6555988 DOI: 10.1186/s40168-019-0703-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/28/2019] [Indexed: 05/21/2023]
30
Voorhuijzen-Harink MM, Hagelaar R, van Dijk JP, Prins TW, Kok EJ, Staats M. Toward on-site food authentication using nanopore sequencing. FOOD CHEMISTRY-X 2019;2:100035. [PMID: 31432019 PMCID: PMC6694865 DOI: 10.1016/j.fochx.2019.100035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/25/2019] [Accepted: 05/23/2019] [Indexed: 11/03/2022]
31
Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates. Antimicrob Agents Chemother 2018;63:AAC.01923-18. [PMID: 30373801 DOI: 10.1128/aac.01923-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/22/2018] [Indexed: 01/19/2023]  Open
32
Golparian D, Donà V, Sánchez-Busó L, Foerster S, Harris S, Endimiani A, Low N, Unemo M. Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer. Sci Rep 2018;8:17596. [PMID: 30514867 PMCID: PMC6279828 DOI: 10.1038/s41598-018-35750-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/10/2018] [Indexed: 11/09/2022]  Open
33
Greig DR, Dallman TJ, Hopkins KL, Jenkins C. MinION nanopore sequencing identifies the position and structure of bacterial antibiotic resistance determinants in a multidrug-resistant strain of enteroaggregative Escherichia coli. Microb Genom 2018;4. [PMID: 30235111 PMCID: PMC6249433 DOI: 10.1099/mgen.0.000213] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
34
Kitsios GD, Fitch A, Manatakis DV, Rapport SF, Li K, Qin S, Huwe J, Zhang Y, Doi Y, Evankovich J, Bain W, Lee JS, Methé B, Benos PV, Morris A, McVerry BJ. Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients. Front Microbiol 2018;9:1413. [PMID: 30042738 PMCID: PMC6048198 DOI: 10.3389/fmicb.2018.01413] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/08/2018] [Indexed: 01/01/2023]  Open
35
Doyle LE, Marsili E. Weak electricigens: A new avenue for bioelectrochemical research. BIORESOURCE TECHNOLOGY 2018;258:354-364. [PMID: 29519634 DOI: 10.1016/j.biortech.2018.02.073] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 05/20/2023]
36
Benítez-Páez A, Sanz Y. Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer. Gigascience 2018;6:1-12. [PMID: 28605506 PMCID: PMC5534310 DOI: 10.1093/gigascience/gix043] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 06/09/2017] [Indexed: 02/07/2023]  Open
37
Brown BL, Watson M, Minot SS, Rivera MC, Franklin RB. MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach. Gigascience 2018;6:1-10. [PMID: 28327976 PMCID: PMC5467020 DOI: 10.1093/gigascience/gix007] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/09/2017] [Indexed: 11/14/2022]  Open
38
Montel F. Séquençage de l’ADN par nanopores. Med Sci (Paris) 2018;34:161-165. [DOI: 10.1051/medsci/20183402014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
39
Xia Y, Li AD, Deng Y, Jiang XT, Li LG, Zhang T. MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage. Front Microbiol 2017;8:2105. [PMID: 29163399 PMCID: PMC5671560 DOI: 10.3389/fmicb.2017.02105] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/16/2017] [Indexed: 11/18/2022]  Open
40
Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B. De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing. THE PLANT CELL 2017;29:2336-2348. [PMID: 29025960 PMCID: PMC5774570 DOI: 10.1105/tpc.17.00521] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/15/2017] [Accepted: 10/11/2017] [Indexed: 05/19/2023]
41
Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev 2017;30:1015-1063. [PMID: 28855266 PMCID: PMC5608882 DOI: 10.1128/cmr.00016-17] [Citation(s) in RCA: 257] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
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Cao Y, Fanning S, Proos S, Jordan K, Srikumar S. A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies. Front Microbiol 2017;8:1829. [PMID: 29033905 PMCID: PMC5627019 DOI: 10.3389/fmicb.2017.01829] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022]  Open
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van der Helm E, Imamovic L, Hashim Ellabaan MM, van Schaik W, Koza A, Sommer MOA. Rapid resistome mapping using nanopore sequencing. Nucleic Acids Res 2017;45:e61. [PMID: 28062856 PMCID: PMC5416750 DOI: 10.1093/nar/gkw1328] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/20/2016] [Indexed: 12/18/2022]  Open
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Li Y, Yang X, Zhao W. Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing. SLAS Technol 2017;22:585-608. [PMID: 28850804 DOI: 10.1177/2472630317727519] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Ludden C, Reuter S, Judge K, Gouliouris T, Blane B, Coll F, Naydenova P, Hunt M, Tracey A, Hopkins KL, Brown NM, Woodford N, Parkhill J, Peacock SJ. Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing. Microb Genom 2017;3:e000114. [PMID: 29026655 PMCID: PMC5605956 DOI: 10.1099/mgen.0.000114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022]  Open
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De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms. Sci Rep 2017. [PMID: 28638050 PMCID: PMC5479803 DOI: 10.1038/s41598-017-03996-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
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George S, Pankhurst L, Hubbard A, Votintseva A, Stoesser N, Sheppard AE, Mathers A, Norris R, Navickaite I, Eaton C, Iqbal Z, Crook DW, Phan HTT. Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches. Microb Genom 2017;3:e000118. [PMID: 29026658 PMCID: PMC5610714 DOI: 10.1099/mgen.0.000118] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/28/2017] [Indexed: 01/31/2023]  Open
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Boža V, Brejová B, Vinař T. DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads. PLoS One 2017;12:e0178751. [PMID: 28582401 PMCID: PMC5459436 DOI: 10.1371/journal.pone.0178751] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 05/18/2017] [Indexed: 12/01/2022]  Open
49
'Omic' Approaches to Study Uropathogenic Escherichia coli Virulence. Trends Microbiol 2017;25:729-740. [PMID: 28550944 DOI: 10.1016/j.tim.2017.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/10/2017] [Accepted: 04/21/2017] [Indexed: 01/21/2023]
50
Klotz AR, Narsimhan V, Soh BW, Doyle PS. Dynamics of DNA Knots during Chain Relaxation. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00287] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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