Artificially designed pathogens – a diagnostic option for future military deployments
Tóm tắt
Diagnostic microbial isolates of bio-safety levels 3 and 4 are difficult to handle in medical field camps under military deployment settings. International transport of such isolates is challenging due to restrictions by the International Air Transport Association. An alternative option might be inactivation and sequencing of the pathogen at the deployment site with subsequent sequence-based revitalization in well-equipped laboratories in the home country for further scientific assessment. A literature review was written based on a PubMed search. First described for poliovirus in 2002, de novo synthesis of pathogens based on their sequence information has become a well-established procedure in science. Successful syntheses have been demonstrated for both viruses and prokaryotes. However, the technology is not yet available for routine diagnostic purposes. Due to the potential utility of diagnostic sequencing and sequence-based de novo synthesis of pathogens, it seems worthwhile to establish the technology for diagnostic purposes over the intermediate term. This is particularly true for resource-restricted deployment settings, where safe handling of harmful pathogens cannot always be guaranteed.
Tài liệu tham khảo
Kelley PW, Takafuji ET, Wiener H, Milhous W, Miller R, Thompson NJ, et al. An outbreak of hookworm infection associated with military operations in Grenada. Mil Med. 1989;154:55–9.
Newton Jr JA, Schnepf GA, Wallace MR, Lobel HO, Kennedy CA, Oldfield 3rd EC. Malaria in US Marines returning from Somalia. JAMA. 1994;272:397–9.
McCarthy M, Estes MK, Hyams KC. Norwalk-like virus infection in military forces: epidemic potential, sporadic disease, and the future direction of prevention and control efforts. J Infect Dis. 2000;181:S387–91.
Ho ZJM, Hwang YFJ, Lee JMV. Emerging and re-emerging infectious diseases: challenges and opportunities for militaries. Mil Med Res. 2014;1:21.
Wever PC, van Bergen L. Death from 1918 pandemic influenza during the First World War: a perspective from personal and anecdotal evidence. Influenza Other Respir Viruses. 2014;8:538–46.
Lawrence DN. Outbreaks of Gastrointestinal Diseases on Cruise Ships: Lessons from Three Decades of Progress. Curr Infect Dis Rep. 2004;6:115–23.
Dill CE, Favata MA. Novel influenza A (H1N1) outbreak on board a US navy vessel. Disaster Med Public Health Prep. 2009;3:S117–20.
Armed Forces Health Surveillance Center (AFHSC). Gastrointestinal infections, active component, U.S. Armed Forces, 2002–2012. MSMR. 2013;20:7–11.
Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, et al. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One. 2011;6:e22751.
Kohl TA, Diel R, Harmsen D, Rothgänger J, Walter KM, Merker M, et al. Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach. J Clin Microbiol. 2014;52:2479–86.
Bhatt AS, Freeman SS, Herrera AF, Pedamallu CS, Gevers D, Duke F, et al. Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome. N Engl J Med. 2013;369:517–28.
Gilbert W, Maxam A. The nucleotide sequence of the lac operator. Proc Natl Acad Sci U S A. 1973;70:3581–4.
Sanger F. The Croonian Lecture, 1975. Nucleotide sequences in DNA. Proc R Soc Lond B Biol Sci. 1975;191:317–33.
Karger BL, Guttman A. DNA sequencing by capillary electrophoresis. Electrophoresis. 2009;30:S196–202.
Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis E. The next generation sequencing revolution and its impact on genomics. Cell. 2013;155:27–38.
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science. 2005;309:1728–32.
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.
Ronaghi M, Pettersson B, Uhlén M, Nyrén P. PCR-introduced loop structure as primer in DNA sequencing. Biotechniques. 1998;25:876–8. 880–2, 884.
Turcatti G, Romieu A, Fedurco M, Tairi AP. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res. 2008;36:e25.
Drmanac S, Kita D, Labat I, Hauser B, Schmidt C, Burczak JD, et al. Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nat Biotechnol. 1998;16:54–8.
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, et al. Single-molecule DNA sequencing of a viral genome. Science. 2008;320:106–9.
Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol. 2008;26:1146–53.
Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30:434–9.
Sherry NL, Porter JL, Seemann T, Watkins A, Stinear TP, Howden BP. Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol. 2013;51:1396–401.
Stemmer WPC, Crameri A, Ha KD, Brennan TM, Heyneker HL. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene. 1995;104:49–53.
Heim J, Ostergaard Tange T, Klein J. Bäckerhefe Saccharomyces cerevisiae als universelle chemische Mikrofabrik. Biospektrum. 2014;20:456 [Article in German].
Kumar A, Snyder M. Emerging technologies in yeast genomics. Nature Rev Genet. 2001;2:203.
Cello J, Paul AV, Wimmer E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 2002;297:1016–8.
Wimmer E. The test-tube synthesis of a chemical called poliovirus: The simple synthesis of a virus has far-reaching societal implications. Embo Rep. 2006;7:S3–9.
Sedova ES, Shcherbinin DN, Migunov AI, Smirnov IA, Diu L, Shmarov MM, et al. Recombinant influenza vaccines. Acta Naturae. 2012;4:17–27.
Pushko P, Pumpens P, Grens E. Development of virus-like particle technology from small highly symmetric to large complex virus-like particle structures. Intervirology. 2013;56:141–56.
Lamb RA, Jackson D. Extinct 1918 virus comes alive. Nature Med. 2005;11:1155.
Wimmer E, Mueller S, Tumpey TM, Taubenberger JK. Synthetic viruses: a new opportunity to understand and prevent viral disease. Nat Biotechnol. 2009;27:1163–72.
Jackson RJ, Ramsay AJ, Christensen CD, Beaton S, Hall DF, Ramshaw IA. Expression of mouse interleukin-4 by a recombinant ectromelia virus surpresses cytolytic lymphocyte responses and overcomes genetic resistance to mousepox. J Virol. 2001;75:1205–10.
Müllbacher A, Lobigs M. Creation of killer poxvirus could have been predicted. J Virol. 2001;75:8353–5.
Finkel E. Engineered mouse virus spurs bioweapon fears. Science. 2001;291:585.
Cheema TA, Fecci PE, Ning J, Rabkin SD. Immunovirotherapy for the treatment of glioblastoma. Oncoimmunology. 2014;3:e27218.
Wirth T, Parker N, Ylä-Herttuala S. History of gene therapy. Gene. 2013;525:162–9.
Lindberg AM, Crowell RL, Zell R, Kandolf R, Pettersson U. Mapping of the RD phenotype of the Nancy strain of coxsack- ievirus B3. Virus Res. 1992;24:187–96.
Schmidtke M, Selinka HC, Heim A, Jahn B, Tonew M, Kandolf R, et al. Attachment of coxsackievirus B3 variants to various cell lines: mapping of phenotypic differences to capsid protein VP1. Virology. 2000;275:77–88.
Zautner AE, Körner U, Henke A, Badorff C, Schmidtke M. Heparan sulfates and coxsackievirus-adenovirus receptor: each one mediates coxsackievirus B3 PD infection. J Virol. 2003;77:10071–7.
Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 2008;319:1215–20.
Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, et al. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci U S A. 2008;105:20404–9.
Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science. 2009;325:1693–6.
Goltermann L, Bentin T. Mega-cloning and the advent of synthetic genomes. Artif DNA PNA XNA. 2010;1:54–7.
Gibson DG. Programming biological operating systems: genome design, assembly and activation. Nat Methods. 2014;11:521–6.
Benders GA, Noskov VN, Denisova EA, Lartigue C, Gibson DG, Assad-Garcia N, et al. Cloning whole bacterial genomes in yeast. Nucleic Acids Res. 2010;38:2558–69.
Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 2010;329:52–6.
Gibson DG. Enzymatic assembly of overlapping DNA fragments. Methods Enzymol. 2011;498:349–61.
Gibson DG. Gene and genome construction in yeast. Curr Protoc Mol Biol. 2011;Chapter 3:Unit3.22. doi: 10.1002/0471142727.mb0322s94.
Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, et al. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci U S A. 2008;105(23):20404–9.
Gibson DG, Smith HO, Hutchison 3rd CA, Venter JC, Merryman C. Chemical synthesis of the mouse mitochondrial genome. Nat Methods. 2010;7:901–3.
Gibson DG, Young L, Chuang RY, Venter JC, Hutchison 3rd CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009;6:343–5.
Forster AC, Church GM. Towards synthesis of a minimal cell. Mol Syst Biol. 2006;2:45.
Forster AC, Church GM. Synthetic biology projects in vitro. Genome Res. 2007;17:1–6.
Jewett MC, Forster AC. Update on designing and building minimal cells. Curr Opin Biotechnol. 2010;21:697–703.