Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data

GigaScience

Volumn 7, Issue 3, 2018, Pages 1-9

  Li, Ruichao ^a   Xie, Miaomiao ^a   Dong, Ning ^a   Lin, Dachuan ^a   Yang, Xuemei ^a   Wong, Marcus Ho Yin ^a   Chan, Edward Wai Chi ^a   Chen, Sheng ^a  

^a HONG KONG POLYTECHNIC UNIVERSITY   (Hong Kong)

Author keywords

De novo assembly; Long reads; Multidrug resistance (MDR) plasmids; Nanopore sequencing

Indexed keywords

PLASMID DNA; BACTERIAL DNA;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL INFECTION; BACTERIAL STRAIN; COST EFFECTIVENESS ANALYSIS; DATA ANALYSIS; DNA BARCODING; FEASIBILITY STUDY; GENE SEQUENCE; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; MULTIDRUG RESISTANCE; NEXT GENERATION SEQUENCING; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; SINGLE MOLECULE IMAGING; TREATMENT FAILURE; WORKFLOW; BACTERIAL GENOME; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; NANOPORE; PROCEDURES;

DNA BARCODING, TAXONOMIC; DNA, BACTERIAL; DRUG RESISTANCE, BACTERIAL; DRUG RESISTANCE, MULTIPLE; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NANOPORES; PLASMIDS; SEQUENCE ANALYSIS, DNA;

EID: 85050721613     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1093/gigascience/gix132     Document Type: Article

References (25)

1. Holmes AH, Moore LS, Sundsfjord A et al. Understanding the mechanisms and drivers of antimicrobial resistance. Lancet 2016;387(10014):176-87
2. Marston HD, Dixon DM, Knisely JM et al. Antimicrobial resistance. JAMA 2016;316(11):1193-204
3. Smillie C, Garcillan-Barcia MP, Francia MV et al. Mobility of plasmids. Microbiol Mol Biol Rev 2010;74(3):434-52
4. Beatson SA, Walker MJ. Tracking antibiotic resistance. Science 2014;345(6203):1454-5
5. Conlan S, Thomas PJ, Deming C et al. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Translat Med 2014;6(254):254ra126. doi:10.1126/scitranslmed.3009845
6. Bayliss SC, Hunt VL, Yokoyama M et al. The use of Oxford Nanopore native barcoding for complete genome assembly. Gigascience 2017; doi:10.1093/gigascience/gix001
7. Ashton PM, Nair S, Dallman T et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 2015;33(3):296-300
8. Huang Y, Yu X, Xie M et al. Widespread dissemination of carbapenem-resistant Escherichia coli sequence type 167 strains harboring bla NDM-5 in clinical settings in China. Antimicrob Agents Chemother 2016;60(7):4364-8
9. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2016;17(6):333-51
10. Punina NV, Makridakis NM, Remnev MA et al. Wholegenome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015;9(1):19. doi:10.1186/s40246-015-0037-z
11. Ashton PM, Nair S, Dallman T et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 2015;33(3):296-300. doi:10.1038/nbt.3103
12. Chin CS, Alexander DH, Marks P et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013;10(6):563-9
13. CaoMD, Nguyen SH, Ganesamoorthy D et al. Scaffolding and completing genome assemblies in real-time with nanopore sequencing. Nat Commun 2017;8:14515
14. Koren S, Walenz BP, Berlin K et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017;27(5):722-36
15. Johnson TJ, Nolan LK. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol Mol Biol Revi 2009;73(4):750-74
16. Conlan S, Park M, Deming C et al. Plasmid dynamics in KPC-positive klebsiella pneumoniae during long-term patient colonization. mBio 2016; doi:10.1128/mBio.00742-16
17. Porse A, Schonning K, Munck C et al. Survival and evolution of a large multidrug resistance plasmid in new clinical bacterial hosts. Mol Biol Evol 2016; doi:10.1093/molbev/msw163
18. Loman NJ, Quinlan AR. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics 2014;30(23):3399-401
19. Wick RR, Judd LM, Gorrie CL et al. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017;13(6):e1005595. doi:10.1371/journal.pcbi.1005595
20. Leggett RM, Heavens D, Caccamo M et al. NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. Bioinformatics 2016;32(1): 142-4
21. Carattoli A, Zankari E, Garcia-Fernandez A et al. In silico detection and typing of plasmids using plasmidfinder and plasmidmultilocus sequence typing. Antimicrob Agents Chemother 2014;58(7):3895-903
22. Zankari E, Hasman H, Cosentino S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012;67(11):2640-4
23. Siguier P, Perochon J, Lestrade L et al. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006;34(90001):D32-6
24. Sturn A, Quackenbush J, Trajanoski Z. Genesis: cluster analysis of microarray data. Bioinformatics 2002;18(1): 207-8
25. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011;27(7): 1009-10