Rapid Detection of Genetic Engineering, Structural Variation, and Antimicrobial Resistance Markers in Bacterial Biothreat Pathogens by Nanopore Sequencing
Widespread release of Bacillus anthracis (anthrax) or Yersinia pestis (plague) would prompt a public health emergency. During an exposure event, high-quality whole genome sequencing (WGS) can identify genetic engineering, including the introduction of antimicrobial resistance (AMR) genes. Here, we d...
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Published in | Scientific reports Vol. 9; no. 1; pp. 13501 - 14 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
London
Nature Publishing Group UK
18.09.2019
Nature Publishing Group |
Subjects | |
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Abstract | Widespread release of
Bacillus anthracis
(anthrax) or
Yersinia pestis
(plague) would prompt a public health emergency. During an exposure event, high-quality whole genome sequencing (WGS) can identify genetic engineering, including the introduction of antimicrobial resistance (AMR) genes. Here, we developed rapid WGS laboratory and bioinformatics workflows using a long-read nanopore sequencer (MinION) for
Y. pestis
(6.5 h) and
B. anthracis
(8.5 h) and sequenced strains with different AMR profiles. Both salt-precipitation and silica-membrane extracted DNA were suitable for MinION WGS using both rapid and field library preparation methods. In replicate experiments, nanopore quality metrics were defined for genome assembly and mutation analysis. AMR markers were correctly detected and >99% coverage of chromosomes and plasmids was achieved using 100,000 raw sequencing reads. While chromosomes and large and small plasmids were accurately assembled, including novel multimeric forms of the
Y. pestis
virulence plasmid, pPCP1, MinION reads were error-prone, particularly in homopolymer regions. MinION sequencing holds promise as a practical, front-line strategy for on-site pathogen characterization to speed the public health response during a biothreat emergency. |
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AbstractList | Widespread release of
Bacillus anthracis
(anthrax) or
Yersinia pestis
(plague) would prompt a public health emergency. During an exposure event, high-quality whole genome sequencing (WGS) can identify genetic engineering, including the introduction of antimicrobial resistance (AMR) genes. Here, we developed rapid WGS laboratory and bioinformatics workflows using a long-read nanopore sequencer (MinION) for
Y. pestis
(6.5 h) and
B. anthracis
(8.5 h) and sequenced strains with different AMR profiles. Both salt-precipitation and silica-membrane extracted DNA were suitable for MinION WGS using both rapid and field library preparation methods. In replicate experiments, nanopore quality metrics were defined for genome assembly and mutation analysis. AMR markers were correctly detected and >99% coverage of chromosomes and plasmids was achieved using 100,000 raw sequencing reads. While chromosomes and large and small plasmids were accurately assembled, including novel multimeric forms of the
Y. pestis
virulence plasmid, pPCP1, MinION reads were error-prone, particularly in homopolymer regions. MinION sequencing holds promise as a practical, front-line strategy for on-site pathogen characterization to speed the public health response during a biothreat emergency. Widespread release of Bacillus anthracis (anthrax) or Yersinia pestis (plague) would prompt a public health emergency. During an exposure event, high-quality whole genome sequencing (WGS) can identify genetic engineering, including the introduction of antimicrobial resistance (AMR) genes. Here, we developed rapid WGS laboratory and bioinformatics workflows using a long-read nanopore sequencer (MinION) for Y. pestis (6.5 h) and B. anthracis (8.5 h) and sequenced strains with different AMR profiles. Both salt-precipitation and silica-membrane extracted DNA were suitable for MinION WGS using both rapid and field library preparation methods. In replicate experiments, nanopore quality metrics were defined for genome assembly and mutation analysis. AMR markers were correctly detected and >99% coverage of chromosomes and plasmids was achieved using 100,000 raw sequencing reads. While chromosomes and large and small plasmids were accurately assembled, including novel multimeric forms of the Y. pestis virulence plasmid, pPCP1, MinION reads were error-prone, particularly in homopolymer regions. MinION sequencing holds promise as a practical, front-line strategy for on-site pathogen characterization to speed the public health response during a biothreat emergency. Abstract Widespread release of Bacillus anthracis (anthrax) or Yersinia pestis (plague) would prompt a public health emergency. During an exposure event, high-quality whole genome sequencing (WGS) can identify genetic engineering, including the introduction of antimicrobial resistance (AMR) genes. Here, we developed rapid WGS laboratory and bioinformatics workflows using a long-read nanopore sequencer (MinION) for Y. pestis (6.5 h) and B. anthracis (8.5 h) and sequenced strains with different AMR profiles. Both salt-precipitation and silica-membrane extracted DNA were suitable for MinION WGS using both rapid and field library preparation methods. In replicate experiments, nanopore quality metrics were defined for genome assembly and mutation analysis. AMR markers were correctly detected and >99% coverage of chromosomes and plasmids was achieved using 100,000 raw sequencing reads. While chromosomes and large and small plasmids were accurately assembled, including novel multimeric forms of the Y. pestis virulence plasmid, pPCP1, MinION reads were error-prone, particularly in homopolymer regions. MinION sequencing holds promise as a practical, front-line strategy for on-site pathogen characterization to speed the public health response during a biothreat emergency. Widespread release of Bacillus anthracis (anthrax) or Yersinia pestis (plague) would prompt a public health emergency. During an exposure event, high-quality whole genome sequencing (WGS) can identify genetic engineering, including the introduction of antimicrobial resistance (AMR) genes. Here, we developed rapid WGS laboratory and bioinformatics workflows using a long-read nanopore sequencer (MinION) for Y. pestis (6.5 h) and B. anthracis (8.5 h) and sequenced strains with different AMR profiles. Both salt-precipitation and silica-membrane extracted DNA were suitable for MinION WGS using both rapid and field library preparation methods. In replicate experiments, nanopore quality metrics were defined for genome assembly and mutation analysis. AMR markers were correctly detected and >99% coverage of chromosomes and plasmids was achieved using 100,000 raw sequencing reads. While chromosomes and large and small plasmids were accurately assembled, including novel multimeric forms of the Y. pestis virulence plasmid, pPCP1, MinION reads were error-prone, particularly in homopolymer regions. MinION sequencing holds promise as a practical, front-line strategy for on-site pathogen characterization to speed the public health response during a biothreat emergency.Widespread release of Bacillus anthracis (anthrax) or Yersinia pestis (plague) would prompt a public health emergency. During an exposure event, high-quality whole genome sequencing (WGS) can identify genetic engineering, including the introduction of antimicrobial resistance (AMR) genes. Here, we developed rapid WGS laboratory and bioinformatics workflows using a long-read nanopore sequencer (MinION) for Y. pestis (6.5 h) and B. anthracis (8.5 h) and sequenced strains with different AMR profiles. Both salt-precipitation and silica-membrane extracted DNA were suitable for MinION WGS using both rapid and field library preparation methods. In replicate experiments, nanopore quality metrics were defined for genome assembly and mutation analysis. AMR markers were correctly detected and >99% coverage of chromosomes and plasmids was achieved using 100,000 raw sequencing reads. While chromosomes and large and small plasmids were accurately assembled, including novel multimeric forms of the Y. pestis virulence plasmid, pPCP1, MinION reads were error-prone, particularly in homopolymer regions. MinION sequencing holds promise as a practical, front-line strategy for on-site pathogen characterization to speed the public health response during a biothreat emergency. |
ArticleNumber | 13501 |
Author | Gargis, Amy S. Sue, David Conley, Andrew B. McLaughlin, Heather P. Cherney, Blake |
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BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31534162$$D View this record in MEDLINE/PubMed |
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Cites_doi | 10.1002/elps.201300174 10.1101/gr.092759.109 10.3201/eid0701.010106 10.1128/JCM.01069-17 10.1093/bioinformatics/btp352 10.1128/JCM.02209-16 10.1038/nmeth.3444 10.1001/jama.283.17.2281 10.1038/nbt.2288 10.1128/AAC.00306-06 10.1038/s41598-017-03996-z 10.1016/j.mimet.2013.08.013 10.1371/journal.pone.0104400 10.1056/NEJM199709043371004 10.12688/f1000research.11354.1 10.1128/mSystems.00154-18 10.1099/00221287-148-6-1687 10.1128/JB.00691-09 10.1101/gr.229202 10.4269/ajtmh.1998.59.679 10.1093/bioinformatics/bty191 10.1016/j.ygeno.2012.06.009 10.1128/JB.01518-09 10.1128/CMR.00033-15 10.1056/NEJMp1713881 10.1186/s12864-018-5381-7 10.1007/978-0-387-72124-8_31 10.1038/s41598-018-29334-5 10.1099/mgen.0.000132 10.1038/nbt.3103 10.3201/eid0706.010604 10.1016/j.ijantimicag.2017.09.015 10.1101/gr.214270.116 10.1038/nrg.2016.49 10.1038/s41587-019-0072-8 10.1093/bib/bbv029 10.1128/AAC.00247-10 10.7717/peerj.761 10.1128/CMR.17.2.434-464.2004 10.1093/bioinformatics/btw152 10.3201/eid0810.020353 10.1093/nar/gkv784 10.1128/JB.185.3.823-830.2003 10.4161/bact.27943 10.1128/JCM.39.10.3649-3655.2001 10.1002/0471250953.bi1112s47 10.1128/AAC.00840-16 10.1146/annurev.micro.62.081307.162832 10.1128/JCM.03251-15 10.1128/AAC.05043-11 10.1038/35097083 10.1016/j.gpb.2016.05.004 10.1038/nature16996 10.1128/AAC.47.7.2362-2365.2003 10.1016/j.cmi.2017.10.013 10.1038/nrmicro730 10.1128/MRA.01122-18 10.1093/nar/gkv1004 10.1155/2010/760819 10.1007/978-1-60327-595-8_44 10.1101/247148 10.1101/530972 10.1093/infdis/73.2.124 10.1001/jama.2018.21669 |
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References | Chen, Succi, Tenover, Koehler (CR7) 2003; 185 Giordano (CR57) 2017; 7 Li (CR61) 2016; 32 Li (CR67) 2009; 25 Cabanel, Bouchier, Rajerison, Carniel (CR16) 2018; 51 CR39 Pomerantsev, Shishkova, Marinin (CR8) 1992; 37 CR37 Lemon, Khil, Frank, Dekker (CR56) 2017; 55 Lindler, Fan, Jahan (CR11) 2001; 39 Loman, Quick, Simpson (CR63) 2015; 12 Li (CR60) 2018; 34 Galimand, Carniel, Courvalin (CR13) 2006; 50 Kolmogorov, Yuan, Lin, Pevzner (CR55) 2019; 37 Urich, Chalcraft, Schriefer, Yockey, Petersen (CR18) 2012; 56 Besser, Carleton, Gerner-Smidt, Lindsey, Trees (CR28) 2018; 24 Achtman (CR49) 2008; 62 Quick (CR42) 2016; 530 Vaser, Sovic, Nagarajan, Sikic (CR62) 2017; 27 Steinberger-Levy (CR21) 2007; 603 McLaughlin, Gargis, Michel, Sue, Weigel (CR23) 2017; 55 Rajanna (CR48) 2010; 2010 Chen, Ye, Zhang, Xu (CR65) 2015; 43 CR4 CR6 Guiyoule (CR14) 2001; 7 Tyler (CR36) 2018; 8 Wren (CR51) 2003; 1 Kleinheinz, Joensen, Larsen (CR64) 2014; 4 Laehnemann, Borkhardt, McHardy (CR29) 2016; 17 CR43 Jain (CR35) 2017; 6 Goldstein, Beka, Graf, Klassen (CR33) 2019; 20 Radnedge, Agron, Worsham, Andersen (CR50) 2002; 148 Weigel, Sue, Michel, Kitchel, Pillai (CR19) 2010; 54 Price (CR9) 2003; 47 Inglesby (CR12) 2000; 283 Wagar (CR1) 2016; 29 Goodwin, McPherson, McCombie (CR24) 2016; 17 Bugrysheva, Lascols, Sue, Weigel (CR22) 2016; 54 Quinlan (CR66) 2014; 47 Schofield (CR20) 2013; 95 Jernigan (CR2) 2002; 8 Lu, Giordano, Ning (CR26) 2016; 14 Stoesser (CR30) 2016; 60 CR17 CR59 CR58 Jernigan (CR3) 2001; 7 O’Donnell, Wang, Dunbar (CR45) 2013; 34 CR54 CR53 Ruan, Feng (CR40) 2016; 44 Wick, Judd, Gorrie, Holt (CR25) 2017; 3 Forde (CR31) 2014; 9 Bashir (CR32) 2012; 30 Chu, Dong, Zhou, Garon (CR38) 1998; 59 Anisimov, Lindler, Pier (CR46) 2004; 17 Ricker, Qian, Fulthorpe (CR27) 2012; 100 Mead (CR5) 2018; 378 Galimand (CR15) 1997; 337 Ashton (CR34) 2015; 33 Gargis (CR72) 2019; 8 Castro-Nallar (CR41) 2015; 3 Gargis (CR44) 2018; 3 Ross, Thomason, Koehler (CR71) 2009; 191 Eppinger (CR47) 2010; 192 Parkhill (CR52) 2001; 413 Krzywinski (CR70) 2009; 19 Ryzhko (CR10) 1994; 39 Kent (CR68) 2002; 12 Delcher, Salzberg, Phillippy (CR69) 2003; Unit 10 Y Chen (49700_CR7) 2003; 185 D Laehnemann (49700_CR29) 2016; 17 49700_CR4 CR O’Donnell (49700_CR45) 2013; 34 49700_CR6 E Wagar (49700_CR1) 2016; 29 A Bashir (49700_CR32) 2012; 30 A Guiyoule (49700_CR14) 2001; 7 E Castro-Nallar (49700_CR41) 2015; 3 RR Wick (49700_CR25) 2017; 3 49700_CR43 L Radnedge (49700_CR50) 2002; 148 MC Chu (49700_CR38) 1998; 59 CL Ross (49700_CR71) 2009; 191 HP McLaughlin (49700_CR23) 2017; 55 49700_CR39 SK Urich (49700_CR18) 2012; 56 49700_CR37 N Ricker (49700_CR27) 2012; 100 Y Chen (49700_CR65) 2015; 43 J Parkhill (49700_CR52) 2001; 413 J Besser (49700_CR28) 2018; 24 M Galimand (49700_CR15) 1997; 337 LM Weigel (49700_CR19) 2010; 54 H Li (49700_CR60) 2018; 34 M Jain (49700_CR35) 2017; 6 M Kolmogorov (49700_CR55) 2019; 37 M Achtman (49700_CR49) 2008; 62 TV Inglesby (49700_CR12) 2000; 283 S Goldstein (49700_CR33) 2019; 20 JA Jernigan (49700_CR3) 2001; 7 AL Delcher (49700_CR69) 2003; Unit 10 PS Mead (49700_CR5) 2018; 378 AS Gargis (49700_CR44) 2018; 3 IV Ryzhko (49700_CR10) 1994; 39 F Giordano (49700_CR57) 2017; 7 WJ Kent (49700_CR68) 2002; 12 AP Pomerantsev (49700_CR8) 1992; 37 AP Anisimov (49700_CR46) 2004; 17 JK Lemon (49700_CR56) 2017; 55 DA Schofield (49700_CR20) 2013; 95 M Galimand (49700_CR13) 2006; 50 49700_CR17 H Li (49700_CR61) 2016; 32 49700_CR59 LB Price (49700_CR9) 2003; 47 R Vaser (49700_CR62) 2017; 27 N Cabanel (49700_CR16) 2018; 51 LE Lindler (49700_CR11) 2001; 39 H Lu (49700_CR26) 2016; 14 C Rajanna (49700_CR48) 2010; 2010 DB Jernigan (49700_CR2) 2002; 8 N Stoesser (49700_CR30) 2016; 60 Z Ruan (49700_CR40) 2016; 44 BM Forde (49700_CR31) 2014; 9 49700_CR58 I Steinberger-Levy (49700_CR21) 2007; 603 49700_CR53 AR Quinlan (49700_CR66) 2014; 47 49700_CR54 PM Ashton (49700_CR34) 2015; 33 AS Gargis (49700_CR72) 2019; 8 KA Kleinheinz (49700_CR64) 2014; 4 AD Tyler (49700_CR36) 2018; 8 M Eppinger (49700_CR47) 2010; 192 NJ Loman (49700_CR63) 2015; 12 J Quick (49700_CR42) 2016; 530 H Li (49700_CR67) 2009; 25 M Krzywinski (49700_CR70) 2009; 19 BW Wren (49700_CR51) 2003; 1 JV Bugrysheva (49700_CR22) 2016; 54 S Goodwin (49700_CR24) 2016; 17 |
References_xml | – volume: 34 start-page: 2137 year: 2013 end-page: 2144 ident: CR45 article-title: Error analysis of idealized nanopore sequencing publication-title: Electrophoresis doi: 10.1002/elps.201300174 contributor: fullname: Dunbar – volume: 19 start-page: 1639 year: 2009 end-page: 1645 ident: CR70 article-title: Circos: an information aesthetic for comparative genomics publication-title: Genome Research doi: 10.1101/gr.092759.109 contributor: fullname: Krzywinski – volume: 7 start-page: 43 year: 2001 end-page: 48 ident: CR14 article-title: Transferable plasmid-mediated resistance to streptomycin in a clinical isolate of publication-title: Emerg Infect Dis doi: 10.3201/eid0701.010106 contributor: fullname: Guiyoule – volume: 55 start-page: 3530 year: 2017 end-page: 3543 ident: CR56 article-title: Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates publication-title: J Clin Microbiol doi: 10.1128/JCM.01069-17 contributor: fullname: Dekker – ident: CR4 – ident: CR39 – volume: 25 start-page: 2078 year: 2009 end-page: 2079 ident: CR67 article-title: The Sequence Alignment/Map format and SAMtools publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btp352 contributor: fullname: Li – volume: 55 start-page: 959 year: 2017 end-page: 970 ident: CR23 article-title: Optical Screening for Rapid Antimicrobial Susceptibility Testing and for Observation of Phenotypic Diversity among Strains of the Genetically Clonal Species publication-title: J Clin Microbiol doi: 10.1128/JCM.02209-16 contributor: fullname: Weigel – volume: 12 start-page: 733 year: 2015 end-page: 735 ident: CR63 article-title: A complete bacterial genome assembled using only nanopore sequencing data publication-title: Nature Methods doi: 10.1038/nmeth.3444 contributor: fullname: Simpson – volume: 283 start-page: 2281 year: 2000 end-page: 2290 ident: CR12 article-title: Plague as a biological weapon: medical and public health management. Working Group on Civilian Biodefense publication-title: JAMA doi: 10.1001/jama.283.17.2281 contributor: fullname: Inglesby – volume: 30 start-page: 701 year: 2012 ident: CR32 article-title: A hybrid approach for the automated finishing of bacterial genomes publication-title: Nature Biotechnology doi: 10.1038/nbt.2288 contributor: fullname: Bashir – volume: 50 start-page: 3233 year: 2006 end-page: 3236 ident: CR13 article-title: Resistance of to antimicrobial agents publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.00306-06 contributor: fullname: Courvalin – volume: 7 year: 2017 ident: CR57 article-title: yeast genome assemblies from MinION, PacBio and MiSeq platforms publication-title: Sci Rep doi: 10.1038/s41598-017-03996-z contributor: fullname: Giordano – volume: 95 start-page: 156 year: 2013 end-page: 161 ident: CR20 article-title: diagnostic detection and rapid antibiotic susceptibility determination using ‘bioluminescent’ reporter phage publication-title: J Microbiol Methods doi: 10.1016/j.mimet.2013.08.013 contributor: fullname: Schofield – volume: 9 start-page: e104400 year: 2014 ident: CR31 article-title: The complete genome sequence of EC958: a high quality reference sequence for the globally disseminated multidrug resistant O25b:H4-ST131 clone publication-title: PLoS ONE doi: 10.1371/journal.pone.0104400 contributor: fullname: Forde – volume: 337 start-page: 677 year: 1997 end-page: 680 ident: CR15 article-title: Multidrug resistance in mediated by a transferable plasmid publication-title: N Engl J Med doi: 10.1056/NEJM199709043371004 contributor: fullname: Galimand – volume: Unit 10 start-page: 13 year: 2003 ident: CR69 article-title: Using MUMmer to identify similar regions in large sequence sets publication-title: Current Protocols in Bioinformatics Chapter 10 contributor: fullname: Phillippy – volume: 6 start-page: 760 year: 2017 ident: CR35 article-title: MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry publication-title: F1000Research doi: 10.12688/f1000research.11354.1 contributor: fullname: Jain – ident: CR54 – ident: CR58 – volume: 3 start-page: e00154 year: 2018 end-page: 18 ident: CR44 article-title: Analysis of Whole-Genome Sequences for the Prediction of Penicillin Resistance and beta-Lactamase Activity in publication-title: mSystems doi: 10.1128/mSystems.00154-18 contributor: fullname: Gargis – volume: 148 start-page: 1687 year: 2002 end-page: 1698 ident: CR50 article-title: Genome plasticity in publication-title: Microbiology doi: 10.1099/00221287-148-6-1687 contributor: fullname: Andersen – volume: 191 start-page: 6683 year: 2009 end-page: 6693 ident: CR71 article-title: An extracytoplasmic function sigma factor controls beta-lactamase gene expression in and other group species publication-title: J Bacteriol doi: 10.1128/JB.00691-09 contributor: fullname: Koehler – volume: 12 start-page: 656 year: 2002 end-page: 664 ident: CR68 article-title: BLAT–the BLAST-like alignment tool publication-title: Genome Research doi: 10.1101/gr.229202 contributor: fullname: Kent – volume: 59 start-page: 679 year: 1998 end-page: 686 ident: CR38 article-title: A cryptic 19-kilobase plasmid associated with U.S. isolates of : a dimer of the 9.5-kilobase plasmid publication-title: The American Journal of Tropical Medicine and Hygiene doi: 10.4269/ajtmh.1998.59.679 contributor: fullname: Garon – volume: 37 start-page: 31 year: 1992 end-page: 34 ident: CR8 article-title: Comparison of therapeutic effects of antibiotics of the tetracycline group in the treatment of anthrax caused by a strain inheriting tet-gene of plasmid pBC16 publication-title: Antibiot Khimioter contributor: fullname: Marinin – volume: 34 start-page: 3094 year: 2018 end-page: 3100 ident: CR60 article-title: Minimap2: pairwise alignment for nucleotide sequences publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/bty191 contributor: fullname: Li – volume: 100 start-page: 167 year: 2012 end-page: 175 ident: CR27 article-title: The limitations of draft assemblies for understanding prokaryotic adaptation and evolution publication-title: Genomics doi: 10.1016/j.ygeno.2012.06.009 contributor: fullname: Fulthorpe – volume: 192 start-page: 1685 year: 2010 end-page: 1699 ident: CR47 article-title: Genome sequence of the deep-rooted strain Angola reveals new insights into the evolution and pangenome of the plague bacterium publication-title: J Bacteriol doi: 10.1128/JB.01518-09 contributor: fullname: Eppinger – volume: 29 start-page: 175 year: 2016 end-page: 189 ident: CR1 article-title: Bioterrorism and the Role of the Clinical Microbiology Laboratory publication-title: Clin Microbiol Rev doi: 10.1128/CMR.00033-15 contributor: fullname: Wagar – volume: 378 start-page: 106 year: 2018 end-page: 108 ident: CR5 article-title: Plague in Madagascar - A Tragic Opportunity for Improving Public Health publication-title: N Engl J Med doi: 10.1056/NEJMp1713881 contributor: fullname: Mead – volume: 20 year: 2019 ident: CR33 article-title: Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing publication-title: BMC Genomics doi: 10.1186/s12864-018-5381-7 contributor: fullname: Klassen – volume: 603 start-page: 339 year: 2007 end-page: 350 ident: CR21 article-title: Enrichment of from blood cultures enables rapid antimicrobial susceptibility determination by flow cytometry publication-title: Adv Exp Med Biol doi: 10.1007/978-0-387-72124-8_31 contributor: fullname: Steinberger-Levy – volume: 8 year: 2018 ident: CR36 article-title: Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications publication-title: Scientific Reports doi: 10.1038/s41598-018-29334-5 contributor: fullname: Tyler – volume: 3 start-page: e000132 year: 2017 ident: CR25 article-title: Completing bacterial genome assemblies with multiplex MinION sequencing publication-title: Microbial genomics doi: 10.1099/mgen.0.000132 contributor: fullname: Holt – volume: 33 start-page: 296 year: 2015 end-page: 300 ident: CR34 article-title: MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island publication-title: Nat Biotechnol doi: 10.1038/nbt.3103 contributor: fullname: Ashton – volume: 7 start-page: 933 year: 2001 end-page: 944 ident: CR3 article-title: Bioterrorism-related inhalational anthrax: the first 10 cases reported in the United States publication-title: Emerg Infect Dis doi: 10.3201/eid0706.010604 contributor: fullname: Jernigan – volume: 51 start-page: 249 year: 2018 end-page: 254 ident: CR16 article-title: Plasmid-mediated doxycycline resistance in a strain isolated from a rat publication-title: Int J Antimicrob Agents doi: 10.1016/j.ijantimicag.2017.09.015 contributor: fullname: Carniel – volume: 27 start-page: 737 year: 2017 end-page: 746 ident: CR62 article-title: Fast and accurate genome assembly from long uncorrected reads publication-title: Genome Research doi: 10.1101/gr.214270.116 contributor: fullname: Sikic – volume: 17 start-page: 333 year: 2016 end-page: 351 ident: CR24 article-title: Coming of age: ten years of next-generation sequencing technologies publication-title: Nature reviews Genetics doi: 10.1038/nrg.2016.49 contributor: fullname: McCombie – volume: 37 start-page: 540 year: 2019 end-page: 546 ident: CR55 article-title: Assembly of long, error-prone reads using repeat graphs publication-title: Nat Biotechnol doi: 10.1038/s41587-019-0072-8 contributor: fullname: Pevzner – volume: 17 start-page: 154 year: 2016 end-page: 179 ident: CR29 article-title: Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction publication-title: Briefings in Bioinformatics doi: 10.1093/bib/bbv029 contributor: fullname: McHardy – volume: 54 start-page: 2793 year: 2010 end-page: 2800 ident: CR19 article-title: A rapid antimicrobial susceptibility test for publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.00247-10 contributor: fullname: Pillai – ident: CR43 – volume: 3 start-page: e761 year: 2015 ident: CR41 article-title: Concordance and discordance of sequence survey methods for molecular epidemiology publication-title: PeerJ doi: 10.7717/peerj.761 contributor: fullname: Castro-Nallar – volume: 17 start-page: 434 year: 2004 end-page: 464 ident: CR46 article-title: Intraspecific diversity of publication-title: Clin Microbiol Rev doi: 10.1128/CMR.17.2.434-464.2004 contributor: fullname: Pier – volume: 32 start-page: 2103 year: 2016 end-page: 2110 ident: CR61 article-title: Minimap and miniasm: fast mapping and assembly for noisy long sequences publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btw152 contributor: fullname: Li – volume: 8 start-page: 1019 year: 2002 end-page: 1028 ident: CR2 article-title: Investigation of bioterrorism-related anthrax, United States, 2001: epidemiologic findings publication-title: Emerg Infect Dis doi: 10.3201/eid0810.020353 contributor: fullname: Jernigan – ident: CR37 – ident: CR53 – volume: 43 start-page: 7762 year: 2015 end-page: 7768 ident: CR65 article-title: High speed BLASTN: an accelerated MegaBLAST search tool publication-title: Nucleic Acids Research doi: 10.1093/nar/gkv784 contributor: fullname: Xu – volume: 185 start-page: 823 year: 2003 end-page: 830 ident: CR7 article-title: Beta-lactamase genes of the penicillin-susceptible Sterne strain publication-title: J Bacteriol doi: 10.1128/JB.185.3.823-830.2003 contributor: fullname: Koehler – volume: 4 start-page: e27943 year: 2014 ident: CR64 article-title: Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and virulence genes in bacteriophage and prophage nucleotide sequences publication-title: Bacteriophage doi: 10.4161/bact.27943 contributor: fullname: Larsen – volume: 39 start-page: 3649 year: 2001 end-page: 3655 ident: CR11 article-title: Detection of ciprofloxacin-resistant by fluorogenic PCR using the LightCycler publication-title: J Clin Microbiol doi: 10.1128/JCM.39.10.3649-3655.2001 contributor: fullname: Jahan – ident: CR6 – volume: 47 start-page: 11.12.11 year: 2014 end-page: 34 ident: CR66 article-title: BEDTools: The Swiss-Army Tool for Genome Feature Analysis publication-title: Current Protocols in Bioinformatics doi: 10.1002/0471250953.bi1112s47 contributor: fullname: Quinlan – volume: 60 start-page: 5068 year: 2016 end-page: 5071 ident: CR30 article-title: First Report of blaIMP-14 on a Plasmid Harboring Multiple Drug Resistance Genes in Sequence Type 131 publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.00840-16 contributor: fullname: Stoesser – volume: 39 start-page: 32 year: 1994 end-page: 36 ident: CR10 article-title: Virulence of rifampicin and quinolone resistant mutants of strains of plague microbe with Fra+ and Fra- phenotypes publication-title: Antibiot Khimioter contributor: fullname: Ryzhko – volume: 62 start-page: 53 year: 2008 end-page: 70 ident: CR49 article-title: Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens publication-title: Annual Review of Microbiology doi: 10.1146/annurev.micro.62.081307.162832 contributor: fullname: Achtman – volume: 54 start-page: 1462 year: 2016 end-page: 1471 ident: CR22 article-title: Rapid Antimicrobial Susceptibility Testing of , , and by Use of Laser Light Scattering Technology publication-title: J Clin Microbiol doi: 10.1128/JCM.03251-15 contributor: fullname: Weigel – volume: 56 start-page: 555 year: 2012 end-page: 558 ident: CR18 article-title: Lack of antimicrobial resistance in isolates from 17 countries in the Americas, Africa, and Asia publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.05043-11 contributor: fullname: Petersen – volume: 413 start-page: 523 year: 2001 end-page: 527 ident: CR52 article-title: Genome sequence of , the causative agent of plague publication-title: Nature doi: 10.1038/35097083 contributor: fullname: Parkhill – volume: 14 start-page: 265 year: 2016 end-page: 279 ident: CR26 article-title: Oxford Nanopore MinION Sequencing and Genome Assembly publication-title: Genomics, Proteomics & Bioinformatics doi: 10.1016/j.gpb.2016.05.004 contributor: fullname: Ning – volume: 530 start-page: 228 year: 2016 end-page: 232 ident: CR42 article-title: Real-time, portable genome sequencing for Ebola surveillance publication-title: Nature doi: 10.1038/nature16996 contributor: fullname: Quick – volume: 47 start-page: 2362 year: 2003 end-page: 2365 ident: CR9 article-title: selection and characterization of mutants with high-level resistance to ciprofloxacin publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.47.7.2362-2365.2003 contributor: fullname: Price – ident: CR17 – volume: 24 start-page: 335 year: 2018 end-page: 341 ident: CR28 article-title: Next-generation sequencing technologies and their application to the study and control of bacterial infections publication-title: Clinical Microbiology and Infection doi: 10.1016/j.cmi.2017.10.013 contributor: fullname: Trees – volume: 1 start-page: 55 year: 2003 end-page: 64 ident: CR51 article-title: The yersiniae–a model genus to study the rapid evolution of bacterial pathogens publication-title: Nature Reviews Microbiology doi: 10.1038/nrmicro730 contributor: fullname: Wren – volume: 8 start-page: e01122 year: 2019 end-page: 18 ident: CR72 article-title: Genome Sequences of Penicillin-Resistant Strains publication-title: Microbiol Resour Announc doi: 10.1128/MRA.01122-18 contributor: fullname: Gargis – volume: 44 start-page: D682 year: 2016 end-page: 687 ident: CR40 article-title: BacWGSTdb, a database for genotyping and source tracking bacterial pathogens publication-title: Nucleic Acids Research doi: 10.1093/nar/gkv1004 contributor: fullname: Feng – volume: 2010 start-page: 760819 year: 2010 ident: CR48 article-title: Characterization of pPCP1 Plasmids in Strains Isolated from the Former Soviet Union publication-title: International Journal of Microbiology doi: 10.1155/2010/760819 contributor: fullname: Rajanna – ident: CR59 – ident: 49700_CR4 – volume: 603 start-page: 339 year: 2007 ident: 49700_CR21 publication-title: Adv Exp Med Biol doi: 10.1007/978-0-387-72124-8_31 contributor: fullname: I Steinberger-Levy – volume: 59 start-page: 679 year: 1998 ident: 49700_CR38 publication-title: The American Journal of Tropical Medicine and Hygiene doi: 10.4269/ajtmh.1998.59.679 contributor: fullname: MC Chu – volume: 191 start-page: 6683 year: 2009 ident: 49700_CR71 publication-title: J Bacteriol doi: 10.1128/JB.00691-09 contributor: fullname: CL Ross – volume: 51 start-page: 249 year: 2018 ident: 49700_CR16 publication-title: Int J Antimicrob Agents doi: 10.1016/j.ijantimicag.2017.09.015 contributor: fullname: N Cabanel – volume: 7 start-page: 933 year: 2001 ident: 49700_CR3 publication-title: Emerg Infect Dis doi: 10.3201/eid0706.010604 contributor: fullname: JA Jernigan – volume: 9 start-page: e104400 year: 2014 ident: 49700_CR31 publication-title: PLoS ONE doi: 10.1371/journal.pone.0104400 contributor: fullname: BM Forde – volume: 43 start-page: 7762 year: 2015 ident: 49700_CR65 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkv784 contributor: fullname: Y Chen – volume: 29 start-page: 175 year: 2016 ident: 49700_CR1 publication-title: Clin Microbiol Rev doi: 10.1128/CMR.00033-15 contributor: fullname: E Wagar – volume: 337 start-page: 677 year: 1997 ident: 49700_CR15 publication-title: N Engl J Med doi: 10.1056/NEJM199709043371004 contributor: fullname: M Galimand – volume: 8 start-page: e01122 year: 2019 ident: 49700_CR72 publication-title: Microbiol Resour Announc doi: 10.1128/MRA.01122-18 contributor: fullname: AS Gargis – volume: 17 start-page: 154 year: 2016 ident: 49700_CR29 publication-title: Briefings in Bioinformatics doi: 10.1093/bib/bbv029 contributor: fullname: D Laehnemann – volume: 413 start-page: 523 year: 2001 ident: 49700_CR52 publication-title: Nature doi: 10.1038/35097083 contributor: fullname: J Parkhill – volume: 17 start-page: 333 year: 2016 ident: 49700_CR24 publication-title: Nature reviews Genetics doi: 10.1038/nrg.2016.49 contributor: fullname: S Goodwin – volume: 8 start-page: 1019 year: 2002 ident: 49700_CR2 publication-title: Emerg Infect Dis doi: 10.3201/eid0810.020353 contributor: fullname: DB Jernigan – volume: 34 start-page: 3094 year: 2018 ident: 49700_CR60 publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/bty191 contributor: fullname: H Li – volume: 2010 start-page: 760819 year: 2010 ident: 49700_CR48 publication-title: International Journal of Microbiology doi: 10.1155/2010/760819 contributor: fullname: C Rajanna – volume: 1 start-page: 55 year: 2003 ident: 49700_CR51 publication-title: Nature Reviews Microbiology doi: 10.1038/nrmicro730 contributor: fullname: BW Wren – volume: 34 start-page: 2137 year: 2013 ident: 49700_CR45 publication-title: Electrophoresis doi: 10.1002/elps.201300174 contributor: fullname: CR O’Donnell – volume: 6 start-page: 760 year: 2017 ident: 49700_CR35 publication-title: F1000Research doi: 10.12688/f1000research.11354.1 contributor: fullname: M Jain – volume: 12 start-page: 733 year: 2015 ident: 49700_CR63 publication-title: Nature Methods doi: 10.1038/nmeth.3444 contributor: fullname: NJ Loman – ident: 49700_CR39 – volume: 14 start-page: 265 year: 2016 ident: 49700_CR26 publication-title: Genomics, Proteomics & Bioinformatics doi: 10.1016/j.gpb.2016.05.004 contributor: fullname: H Lu – volume: 32 start-page: 2103 year: 2016 ident: 49700_CR61 publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btw152 contributor: fullname: H Li – volume: 50 start-page: 3233 year: 2006 ident: 49700_CR13 publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.00306-06 contributor: fullname: M Galimand – volume: 17 start-page: 434 year: 2004 ident: 49700_CR46 publication-title: Clin Microbiol Rev doi: 10.1128/CMR.17.2.434-464.2004 contributor: fullname: AP Anisimov – volume: 24 start-page: 335 year: 2018 ident: 49700_CR28 publication-title: Clinical Microbiology and Infection doi: 10.1016/j.cmi.2017.10.013 contributor: fullname: J Besser – volume: 192 start-page: 1685 year: 2010 ident: 49700_CR47 publication-title: J Bacteriol doi: 10.1128/JB.01518-09 contributor: fullname: M Eppinger – volume: 19 start-page: 1639 year: 2009 ident: 49700_CR70 publication-title: Genome Research doi: 10.1101/gr.092759.109 contributor: fullname: M Krzywinski – volume: 47 start-page: 2362 year: 2003 ident: 49700_CR9 publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.47.7.2362-2365.2003 contributor: fullname: LB Price – volume: 25 start-page: 2078 year: 2009 ident: 49700_CR67 publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btp352 contributor: fullname: H Li – ident: 49700_CR6 doi: 10.1007/978-1-60327-595-8_44 – volume: 55 start-page: 959 year: 2017 ident: 49700_CR23 publication-title: J Clin Microbiol doi: 10.1128/JCM.02209-16 contributor: fullname: HP McLaughlin – volume: 12 start-page: 656 year: 2002 ident: 49700_CR68 publication-title: Genome Research doi: 10.1101/gr.229202 contributor: fullname: WJ Kent – volume: 39 start-page: 3649 year: 2001 ident: 49700_CR11 publication-title: J Clin Microbiol doi: 10.1128/JCM.39.10.3649-3655.2001 contributor: fullname: LE Lindler – volume: 7 start-page: 43 year: 2001 ident: 49700_CR14 publication-title: Emerg Infect Dis doi: 10.3201/eid0701.010106 contributor: fullname: A Guiyoule – volume: 30 start-page: 701 year: 2012 ident: 49700_CR32 publication-title: Nature Biotechnology doi: 10.1038/nbt.2288 contributor: fullname: A Bashir – ident: 49700_CR17 – ident: 49700_CR59 – volume: 20 year: 2019 ident: 49700_CR33 publication-title: BMC Genomics doi: 10.1186/s12864-018-5381-7 contributor: fullname: S Goldstein – ident: 49700_CR53 doi: 10.1101/247148 – ident: 49700_CR54 doi: 10.1101/530972 – volume: 27 start-page: 737 year: 2017 ident: 49700_CR62 publication-title: Genome Research doi: 10.1101/gr.214270.116 contributor: fullname: R Vaser – volume: 54 start-page: 2793 year: 2010 ident: 49700_CR19 publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.00247-10 contributor: fullname: LM Weigel – volume: 56 start-page: 555 year: 2012 ident: 49700_CR18 publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.05043-11 contributor: fullname: SK Urich – volume: 100 start-page: 167 year: 2012 ident: 49700_CR27 publication-title: Genomics doi: 10.1016/j.ygeno.2012.06.009 contributor: fullname: N Ricker – volume: 148 start-page: 1687 year: 2002 ident: 49700_CR50 publication-title: Microbiology doi: 10.1099/00221287-148-6-1687 contributor: fullname: L Radnedge – volume: 283 start-page: 2281 year: 2000 ident: 49700_CR12 publication-title: JAMA doi: 10.1001/jama.283.17.2281 contributor: fullname: TV Inglesby – volume: 8 year: 2018 ident: 49700_CR36 publication-title: Scientific Reports doi: 10.1038/s41598-018-29334-5 contributor: fullname: AD Tyler – volume: 3 start-page: e00154 year: 2018 ident: 49700_CR44 publication-title: mSystems doi: 10.1128/mSystems.00154-18 contributor: fullname: AS Gargis – volume: 3 start-page: e000132 year: 2017 ident: 49700_CR25 publication-title: Microbial genomics doi: 10.1099/mgen.0.000132 contributor: fullname: RR Wick – ident: 49700_CR37 doi: 10.1093/infdis/73.2.124 – volume: 44 start-page: D682 year: 2016 ident: 49700_CR40 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkv1004 contributor: fullname: Z Ruan – volume: 39 start-page: 32 year: 1994 ident: 49700_CR10 publication-title: Antibiot Khimioter contributor: fullname: IV Ryzhko – volume: 54 start-page: 1462 year: 2016 ident: 49700_CR22 publication-title: J Clin Microbiol doi: 10.1128/JCM.03251-15 contributor: fullname: JV Bugrysheva – volume: 60 start-page: 5068 year: 2016 ident: 49700_CR30 publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.00840-16 contributor: fullname: N Stoesser – volume: 7 year: 2017 ident: 49700_CR57 publication-title: Sci Rep doi: 10.1038/s41598-017-03996-z contributor: fullname: F Giordano – volume: 37 start-page: 31 year: 1992 ident: 49700_CR8 publication-title: Antibiot Khimioter contributor: fullname: AP Pomerantsev – volume: 33 start-page: 296 year: 2015 ident: 49700_CR34 publication-title: Nat Biotechnol doi: 10.1038/nbt.3103 contributor: fullname: PM Ashton – volume: 185 start-page: 823 year: 2003 ident: 49700_CR7 publication-title: J Bacteriol doi: 10.1128/JB.185.3.823-830.2003 contributor: fullname: Y Chen – ident: 49700_CR58 – volume: 95 start-page: 156 year: 2013 ident: 49700_CR20 publication-title: J Microbiol Methods doi: 10.1016/j.mimet.2013.08.013 contributor: fullname: DA Schofield – volume: 47 start-page: 11.12.11 year: 2014 ident: 49700_CR66 publication-title: Current Protocols in Bioinformatics doi: 10.1002/0471250953.bi1112s47 contributor: fullname: AR Quinlan – volume: 37 start-page: 540 year: 2019 ident: 49700_CR55 publication-title: Nat Biotechnol doi: 10.1038/s41587-019-0072-8 contributor: fullname: M Kolmogorov – volume: 378 start-page: 106 year: 2018 ident: 49700_CR5 publication-title: N Engl J Med doi: 10.1056/NEJMp1713881 contributor: fullname: PS Mead – volume: 62 start-page: 53 year: 2008 ident: 49700_CR49 publication-title: Annual Review of Microbiology doi: 10.1146/annurev.micro.62.081307.162832 contributor: fullname: M Achtman – volume: Unit 10 start-page: 13 year: 2003 ident: 49700_CR69 publication-title: Current Protocols in Bioinformatics Chapter 10 contributor: fullname: AL Delcher – volume: 530 start-page: 228 year: 2016 ident: 49700_CR42 publication-title: Nature doi: 10.1038/nature16996 contributor: fullname: J Quick – volume: 3 start-page: e761 year: 2015 ident: 49700_CR41 publication-title: PeerJ doi: 10.7717/peerj.761 contributor: fullname: E Castro-Nallar – ident: 49700_CR43 doi: 10.1001/jama.2018.21669 – volume: 4 start-page: e27943 year: 2014 ident: 49700_CR64 publication-title: Bacteriophage doi: 10.4161/bact.27943 contributor: fullname: KA Kleinheinz – volume: 55 start-page: 3530 year: 2017 ident: 49700_CR56 publication-title: J Clin Microbiol doi: 10.1128/JCM.01069-17 contributor: fullname: JK Lemon |
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Bacillus anthracis
(anthrax) or
Yersinia pestis
(plague) would prompt a public health emergency. During an exposure event, high-quality... Widespread release of Bacillus anthracis (anthrax) or Yersinia pestis (plague) would prompt a public health emergency. During an exposure event, high-quality... Abstract Widespread release of Bacillus anthracis (anthrax) or Yersinia pestis (plague) would prompt a public health emergency. During an exposure event,... |
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SubjectTerms | 45 45/22 45/23 631/1647/2234 631/1647/514/2254 631/326/2521 Anthrax Anti-Bacterial Agents - pharmacology Antimicrobial agents Antimicrobial resistance Bacteria - genetics Bioinformatics Chromosomes Computational Biology - methods Drug resistance Drug Resistance, Bacterial - genetics Drug Resistance, Microbial - genetics Genetic diversity Genetic Engineering Genome, Bacterial - drug effects Genomes Genomics - methods High-Throughput Nucleotide Sequencing - methods Humanities and Social Sciences multidisciplinary Nanopore Sequencing - methods Pathogens Plague Plasmids Public health Science Science (multidisciplinary) Sequence Analysis, DNA - methods Silica Virulence Virulence - drug effects Whole Genome Sequencing - methods |
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Title | Rapid Detection of Genetic Engineering, Structural Variation, and Antimicrobial Resistance Markers in Bacterial Biothreat Pathogens by Nanopore Sequencing |
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