Next generation sequencing technologies and the changing landscape of phage genomics

References

• Summers WC. Bacteriophage therapy. Annu Rev Microbiol 2001; 55:437 - 51; http://dx.doi.org/10.1146/annurev.micro.55.1.437; PMID: 11544363
   PubMed Web of Science ®Google Scholar
• Sulakvelidze A. Phage therapy: an attractive option for dealing with antibiotic-resistant bacterial infections. Drug Discov Today 2005; 10:807 - 9; http://dx.doi.org/10.1016/S1359-6446(05)03441-0; PMID: 15970258
   PubMed Web of Science ®Google Scholar
• Sulakvelidze A, Alavidze Z, Morris JG Jr.. Bacteriophage therapy. Antimicrob Agents Chemother 2001; 45:649 - 59; http://dx.doi.org/10.1128/AAC.45.3.649-659.2001; PMID: 11181338
   PubMed Web of Science ®Google Scholar
• Fischetti VA. Bacteriophage endolysins: a novel anti-infective to control Gram-positive pathogens. Int J Med Microbiol 2010; 300:357 - 62; http://dx.doi.org/10.1016/j.ijmm.2010.04.002; PMID: 20452280
   PubMed Web of Science ®Google Scholar
• Loessner MJ. Bacteriophage endolysins--current state of research and applications. Curr Opin Microbiol 2005; 8:480 - 7; http://dx.doi.org/10.1016/j.mib.2005.06.002; PMID: 15979390
   PubMed Web of Science ®Google Scholar
• Summers W. Bacteriophage research: early history. In: Kutter E, Sulakvelidze A, eds. Bacteriophages: Biology and Applications. Boca Raton, FL: CRC Press, 2005:5-27.
   Google Scholar
• Projan S. Phage-inspired antibiotics?. Nat Biotechnol 2004; 22:167 - 8; http://dx.doi.org/10.1038/nbt0204-167; PMID: 14755287
   PubMed Web of Science ®Google Scholar
• Anany H, Chen W, Pelton R, Griffiths MW. Biocontrol of Listeria monocytogenes and Escherichia coli O157:H7 in meat by using phages immobilized on modified cellulose membranes. Appl Environ Microbiol 2011; 77:6379 - 87; http://dx.doi.org/10.1128/AEM.05493-11; PMID: 21803890
   PubMed Web of Science ®Google Scholar
• Callaway TR, Edrington TS, Brabban AD, Anderson RC, Rossman ML, Engler MJ, et al. Bacteriophage isolated from feedlot cattle can reduce Escherichia coli O157:H7 populations in ruminant gastrointestinal tracts. Foodborne Pathog Dis 2008; 5:183 - 91; http://dx.doi.org/10.1089/fpd.2007.0057; PMID: 18407757
   PubMed Web of Science ®Google Scholar
• Guenther S, Herzig O, Fieseler L, Klumpp J, Loessner MJ. Biocontrol of Salmonella Typhimurium in RTE foods with the virulent bacteriophage FO1-E2. Int J Food Microbiol 2012; 154:66 - 72; http://dx.doi.org/10.1016/j.ijfoodmicro.2011.12.023; PMID: 22244192
   PubMed Web of Science ®Google Scholar
• Guenther S, Huwyler D, Richard S, Loessner MJ. Virulent bacteriophage for efficient biocontrol of Listeria monocytogenes in ready-to-eat foods. Appl Environ Microbiol 2009; 75:93 - 100; http://dx.doi.org/10.1128/AEM.01711-08; PMID: 19011076
   PubMed Web of Science ®Google Scholar
• Hooton SP, Atterbury RJ, Connerton IF. Application of a bacteriophage cocktail to reduce Salmonella Typhimurium U288 contamination on pig skin. Int J Food Microbiol 2011; 151:157 - 63; http://dx.doi.org/10.1016/j.ijfoodmicro.2011.08.015; PMID: 21899907
   PubMed Web of Science ®Google Scholar
• Patel J, Sharma M, Millner P, Calaway T, Singh M. Inactivation of Escherichia coli O157:H7 attached to spinach harvester blade using bacteriophage. Foodborne Pathog Dis 2011; 8:541 - 6; http://dx.doi.org/10.1089/fpd.2010.0734; PMID: 21453119
   PubMed Web of Science ®Google Scholar
• Callewaert L, Walmagh M, Michiels CW, Lavigne R. Food applications of bacterial cell wall hydrolases. Curr Opin Biotechnol 2011; 22:164 - 71; http://dx.doi.org/10.1016/j.copbio.2010.10.012; PMID: 21093250
   PubMed Web of Science ®Google Scholar
• Fenton M, Ross P, McAuliffe O, O’Mahony J, Coffey A. Recombinant bacteriophage lysins as antibacterials. Bioeng Bugs 2010; 1:9 - 16; http://dx.doi.org/10.4161/bbug.1.1.9818; PMID: 21327123
   PubMedGoogle Scholar
• Pierce CL, Rees JC, Fernández FM, Barr JR. Detection of Staphylococcus aureus using 15N-labeled bacteriophage amplification coupled with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Anal Chem 2011; 83:2286 - 93; http://dx.doi.org/10.1021/ac103024m; PMID: 21341703
   PubMed Web of Science ®Google Scholar
• Rees JC, Voorhees KJ. Simultaneous detection of two bacterial pathogens using bacteriophage amplification coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2005; 19:2757 - 61; http://dx.doi.org/10.1002/rcm.2107; PMID: 16136521
   PubMed Web of Science ®Google Scholar
• Griffiths MW. Phage-Based Methods for the Detection of Bacterial Pathogens. In: Sabour PM, Griffiths MW, eds. Bacteriophage in the control of Food- and Waterborne Pathogens. Washington, DC: ASM Press, 2010:31-61.
   Google Scholar
• Smartt AE, Ripp S. Bacteriophage reporter technology for sensing and detecting microbial targets. Anal Bioanal Chem 2011; 400:991 - 1007; http://dx.doi.org/10.1007/s00216-010-4561-3; PMID: 21165607
   PubMed Web of Science ®Google Scholar
• Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437:376 - 80; PMID: 16056220
   PubMed Web of Science ®Google Scholar
• Rasko DA, Altherr MR, Han CS, Ravel J. Genomics of the Bacillus cereus group of organisms. FEMS Microbiol Rev 2005; 29:303 - 29; PMID: 15808746
   PubMed Web of Science ®Google Scholar
• Hagens S, Loessner MJ. Bacteriophage for biocontrol of foodborne pathogens: calculations and considerations. Curr Pharm Biotechnol 2010; 11:58 - 68; http://dx.doi.org/10.2174/138920110790725429; PMID: 20214608
   PubMed Web of Science ®Google Scholar
• Merabishvili M, Pirnay JP, Verbeken G, Chanishvili N, Tediashvili M, Lashkhi N, et al. Quality-controlled small-scale production of a well-defined bacteriophage cocktail for use in human clinical trials. PLoS One 2009; 4:e4944; http://dx.doi.org/10.1371/journal.pone.0004944; PMID: 19300511
   PubMed Web of Science ®Google Scholar
• Carlton RM, Noordman WH, Biswas B, de Meester ED, Loessner MJ. Bacteriophage P100 for control of Listeria monocytogenes in foods: genome sequence, bioinformatic analyses, oral toxicity study, and application. Regul Toxicol Pharmacol 2005; 43:301 - 12; http://dx.doi.org/10.1016/j.yrtph.2005.08.005; PMID: 16188359
   PubMed Web of Science ®Google Scholar
• Buckingham SD. Next Generation Data Explosion. Lab Times 2010; 1:52 - 3
   Google Scholar
• Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 2012; 30:295 - 6; http://dx.doi.org/10.1038/nbt0412-295; PMID: 22491260
   PubMed Web of Science ®Google Scholar
• Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, et al. Genomics. Genome project standards in a new era of sequencing. Science 2009; 326:236 - 7; http://dx.doi.org/10.1126/science.1180614; PMID: 19815760
   PubMed Web of Science ®Google Scholar
• Hatfull GF. Bacteriophage genomics. Curr Opin Microbiol 2008; 11:447 - 53; http://dx.doi.org/10.1016/j.mib.2008.09.004; PMID: 18824125
   PubMed Web of Science ®Google Scholar
• Casjens S, Gilcrease EB. Determining DNA Packaging Stragety by Analysis of the Termini of the Chromosomes in Tailed-Bacteriophage Virions. In: Clokie MRJ, Kropinski A, eds. Bacteriophages - Methods and Protocols Volume 2: Molecular and Applied Aspects. New York: Humana Press, 2009:91-111.
   Google Scholar
• Klumpp J, Dorscht J, Lurz R, Bielmann R, Wieland M, Zimmer M, et al. The terminally redundant, nonpermuted genome of Listeria bacteriophage A511: a model for the SPO1-like myoviruses of gram-positive bacteria. J Bacteriol 2008; 190:5753 - 65; http://dx.doi.org/10.1128/JB.00461-08; PMID: 18567664
   PubMed Web of Science ®Google Scholar
• Hendrix RW, Hatfull GF, Smith MC. Bacteriophages with tails: chasing their origins and evolution. Res Microbiol 2003; 154:253 - 7; http://dx.doi.org/10.1016/S0923-2508(03)00068-8; PMID: 12798229
   PubMed Web of Science ®Google Scholar
• Sambrook J, Russell DW. Molecular Cloning - A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press, 2001.
   Google Scholar
• Lech K. Preparing Lambda DNA from phage lysates. In: Ausubel FM, Brent R, Kingston RE, Moore DD, G. SJ, Smith JA, eds. Current Protocols in Molecular Biology. New York: John Wiley & Sons Inc., 1990.
   Google Scholar
• Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 2001; 11:1095 - 9; http://dx.doi.org/10.1101/gr.180501; PMID: 11381035
   PubMed Web of Science ®Google Scholar
• Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, Sengamalay N, et al. Viral genome sequencing by random priming methods. BMC Genomics 2008; 9:5; http://dx.doi.org/10.1186/1471-2164-9-5; PMID: 18179705
   PubMed Web of Science ®Google Scholar
• Reyes GR, Kim JP. Sequence-independent, single-primer amplification (SISPA) of complex DNA populations. Mol Cell Probes 1991; 5:473 - 81; http://dx.doi.org/10.1016/S0890-8508(05)80020-9; PMID: 1664049
   PubMed Web of Science ®Google Scholar
• Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, et al. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.. Science 2001; 293:498 - 506; http://dx.doi.org/10.1126/science.1061217; PMID: 11463916
   PubMed Web of Science ®Google Scholar
• Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8:186 - 94; PMID: 9521922
   PubMed Web of Science ®Google Scholar
• Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8:175 - 85; PMID: 9521921
   PubMed Web of Science ®Google Scholar
• Li M, Nordborg M, Li LM. Adjust quality scores from alignment and improve sequencing accuracy. Nucleic Acids Res 2004; 32:5183 - 91; http://dx.doi.org/10.1093/nar/gkh850; PMID: 15459287
   PubMed Web of Science ®Google Scholar
• Fouts DE, Rasko DA, Cer RZ, Jiang L, Fedorova NB, Shvartsbeyn A, et al. Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry. J Bacteriol 2006; 188:3402 - 8; http://dx.doi.org/10.1128/JB.188.9.3402-3408.2006; PMID: 16621835
   PubMed Web of Science ®Google Scholar
• Dorscht J, Klumpp J, Bielmann R, Schmelcher M, Born Y, Zimmer M, et al. Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site. J Bacteriol 2009; 191:7206 - 15; http://dx.doi.org/10.1128/JB.01041-09; PMID: 19783628
   PubMed Web of Science ®Google Scholar
• Klumpp J, Calendar R, Loessner MJ. Complete Nucleotide Sequence and Molecular Characterization of Bacillus Phage TP21 and its Relatedness to Other Phages with the Same Name. Viruses 2010; 2:961 - 71; http://dx.doi.org/10.3390/v2040961; PMID: 21994663
   PubMed Web of Science ®Google Scholar
• Stevens RH, Ektefaie MR, Fouts DE. The annotated complete DNA sequence of Enterococcus faecalis bacteriophage φEf11 and its comparison with all available phage and predicted prophage genomes. FEMS Microbiol Lett 2011; 317:9 - 26; http://dx.doi.org/10.1111/j.1574-6968.2010.02203.x; PMID: 21204936
   PubMed Web of Science ®Google Scholar
• Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008; 5:235 - 7; http://dx.doi.org/10.1038/nmeth.1184; PMID: 18264105
   PubMed Web of Science ®Google Scholar
• Kumar S, Blaxter ML. Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 2010; 11:571; http://dx.doi.org/10.1186/1471-2164-11-571; PMID: 20950480
   PubMed Web of Science ®Google Scholar
• Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, et al. A whole-genome assembly of Drosophila.. Science 2000; 287:2196 - 204; http://dx.doi.org/10.1126/science.287.5461.2196; PMID: 10731133
   PubMed Web of Science ®Google Scholar
• Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 2012; 30:693 - 700; http://dx.doi.org/10.1038/nbt.2280; PMID: 22750884
   PubMed Web of Science ®Google Scholar
• Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011; 365:709 - 17; http://dx.doi.org/10.1056/NEJMoa1106920; PMID: 21793740
   PubMed Web of Science ®Google Scholar
• Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009; 323:133 - 8; http://dx.doi.org/10.1126/science.1162986; PMID: 19023044
   PubMed Web of Science ®Google Scholar
• Travers KJ, Chin CS, Rank DR, Eid JS, Turner SW. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 2010; 38:e159; http://dx.doi.org/10.1093/nar/gkq543; PMID: 20571086
   PubMedGoogle Scholar
• Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, et al. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004; 14:1147 - 59; http://dx.doi.org/10.1101/gr.1917404; PMID: 15140833
   PubMed Web of Science ®Google Scholar
• Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821 - 9; http://dx.doi.org/10.1101/gr.074492.107; PMID: 18349386
   PubMed Web of Science ®Google Scholar
• Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010; 95:315 - 27; http://dx.doi.org/10.1016/j.ygeno.2010.03.001; PMID: 20211242
   PubMed Web of Science ®Google Scholar
• Schmuki MM, Erne D, Loessner MJ, Klumpp J. Bacteriophage P70: Unique morphology and unrelatedness to other Listeria bacteriophages.. J Virol 2012; 86
   PubMed Web of Science ®Google Scholar