Rapid Focused Sequencing: A Multiplexed Assay for Simultaneous Detection and Strain Typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Turingan, Rosemary S ^a   Thomann, Hans Ulrich ^a   Zolotova, Anna ^a   Tan, Eugene ^a   Selden, Richard F ^a  

^a NetBio   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLICON; ARTICLE; BACILLUS ANTHRACIS; BACTERIAL VIRULENCE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; DNA SEQUENCE; ELECTROPHORESIS; FLUORESCENCE ANALYSIS; FRANCISELLA TULARENSIS; GENE AMPLIFICATION; GENOME SIZE; MICROFLUIDIC ANALYSIS; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; PROCESS DEVELOPMENT; YERSINIA PESTIS;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; BACILLUS ANTHRACIS; BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; BIOTERRORISM; DNA PRIMERS; DNA, BACTERIAL; FRANCISELLA TULARENSIS; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; YERSINIA PESTIS;

EID: 84873898357     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0056093     Document Type: Article

References (61)

1. Graham B, Talent JM, Allison GT (2008) World at risk: the report of the Commission on the Prevention of WMD Proliferation and Terrorism: Vintage.
2. O'Toole T, Inglesby T, (2009) Strategic priorities for US biosecurity. Biosecurity and Bioterrorism 7: 25-28.
3. Eubanks LM, Dickerson TJ, Janda KD, (2007) Technological advancements for the detection of and protection against biological and chemical warfare agents. Chem Soc Rev 36: 458-470.
4. Lim DV, Simpson JM, Kearns EA, Kramer MF (2005) Current and developing technologies for monitoring agents of bioterrorism and biowarfare. Clin Microbiol Rev. 583-607.
5. Bode E, Hurtle W, Norwood D (2004) Real-time PCR assay for a unique chromosomal sequence of Bacillus anthracis. Journal of Clinical Microbiology. 5825-5831.
6. Larsson P, Svensson K, Karlsson L, Guala D, Granberg M, et al. (2007) Canonical insertion-deletion markers for rapid DNA typing of Francisella tularensis. Emerging infectious diseases 13: 1725.
7. Tomioka K, Peredelchuk M, Zhu X, Arena R, Volokhov D, et al. (2005) A multiplex polymerase chain reaction microarray assay to detect bioterror pathogens in blood. The Journal of molecular diagnostics: JMD 7: 486.
8. Tomaso H, Reisinger EC, Al Dahouk S, Frangoulidis D, Rakin A, et al. (2003) Rapid detection of Yersinia pestis with multiplex real-time PCR assays using fluorescent hybridisation probes. FEMS Immunology and Medical Microbiology 38: 117-126.
9. Stewart A, Satterfield B, Cohen M, O'Neill K, Robison R, (2008) A quadruplex real-time PCR assay for the detection of Yersinia pestis and its plasmids. Journal of medical microbiology 57: 324-331.
10. Ingmar J, Raditijo H, Jasper B (2010) Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification.
11. Janse I, Bok JM, Hamidjaja RA, Hodemaekers HM, van Rotterdam BJ, (2012) Development and Comparison of Two Assay Formats for Parallel Detection of Four Biothreat Pathogens by Using Suspension Microarrays. PLoS One 7: e31958.
12. Wilson WJ, Erler AM, Nasarabadi SL, Skowronski EW, Imbro PM (2005) A multiplexed PCR-coupled liquid bead array for the simultaneous detection of four biothreat agents. Mol Cell Probes. 137-144.
13. Giese H, Lam R, Selden R, Tan E, (2009) Fast multiplexed polymerase chain reaction for conventional and microfluidic short tandem repeat analysis. J Forensic Sci 54: 1287-1296.
14. Schumm J, Gutierrez-Mateo C, Tan E, Selden RF (2012) A 27-Locus STR Assay to Meet All United States and European Law Enforcement Agency Standards*. Journal of Forensic Science. In Press.
15. Harrell LJ, Andersen GL, Wilson KH, (1995) Genetic variability of Bacillus anthracis and related species. Journal of clinical microbiology 33: 1847.
16. Keim P, Gruendike JM, Klevytska AM, Schupp JM, Challacombe J, et al. (2009) The genome and variation of Bacillus anthracis. Molecular aspects of medicine 30: 397-405.
17. Price LB, Hugh-Jones M, Jackson PJ, Keim P, (1999) Genetic diversity in the protective antigen gene of Bacillus anthracis. Journal of bacteriology 181: 2358.
18. Jensen G, Hansen B, Eilenberg J, Mahillon J, (2003) The hidden lifestyles of Bacillus cereus and relatives. Environmental Microbiology 5: 631-640.
19. Helgason E, Okstad OA, Caugant DA, Johansen HA, Fouet A, et al. (2000) Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis-one species on the basis of genetic evidence. Applied and Environmental Microbiology 66: 2627-2630.
20. Bavykin SG, Lysov YP, Zakhariev V, Kelly JJ, Jackman J, et al. (2004) Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms. Journal of clinical microbiology 42: 3711.
21. Helgason E, Tourasse NJ, Meisal R, Caugant DA, Kolsto AB, (2004) Multilocus sequence typing scheme for bacteria of the Bacillus cereus group. Applied and Environmental Microbiology 70: 191-201.
22. Daffonchio D, Raddadi N, Merabishvili M, Cherif A, Carmagnola L, et al. (2006) Strategy for identification of Bacillus cereus and Bacillus thuringiensis strains closely related to Bacillus anthracis. Applied and Environmental Microbiology 72: 1295.
23. Keim P, Kalif A, Schupp J, Hill K, Travis SE, et al. (1997) Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers. Journal of bacteriology 179: 818.
24. Jackson PJ, Hill K, Laker M, Ticknor L, Keim P, (1999) Genetic comparison of Bacillus anthracis and its close relatives using amplified fragment length polymorphism and polymerase chain reaction analysis. Journal of applied microbiology 87: 263-269.
25. Lista F, Faggioni G, Valjevac S, Ciammaruconi A, Vaissaire J, et al. (2006) Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis. BMC microbiology 6: 33.
26. Sjostedt A (2003) Family XVII, Francisellaceae. Genus I, Francisella. Bergey's Manual of Systematic Bacteriology. New York, NY: Springer-Verlag. 111-113.
27. Cross J, Penn R (2000) Francisella tularensis (tularemia). Principles and Practice of Infectious Diseases Philadelphia, Pa: Churchill Livingstone. 2393-2402.
28. Nubel U, Reissbrodt R, Weller A, Grunow R, Porsch-Ozcurumez M, et al. (2006) Population structure of Francisella tularensis. Journal of bacteriology 188: 5319.
29. Forsman M, Sandstrom G, Sjostedt A, (1994) Analysis of 16S ribosomal DNA sequences of Francisella strains and utilization for determination of the phylogeny of the genus and for identification of strains by PCR. International journal of systematic bacteriology 44: 38-46.
30. Splettstoesser W, Seibold E, Zeman E, Trebesius K, Podbielski A, (2010) Rapid differentiation of Francisella species and subspecies by fluorescent in situ hybridization targeting the 23S rRNA. BMC microbiology 10: 72.
31. Svensson K, Larsson P, Johansson D, Bystrom M, Forsman M, et al. (2005) Evolution of subspecies of Francisella tularensis. Journal of bacteriology 187: 3903.
32. La Scola B, Elkarkouri K, Li W, Wahab T, Fournous G, et al. (2008) Rapid comparative genomic analysis for clinical microbiology: the Francisella tularensis paradigm. Genome research 18: 742-750.
33. Farlow J, Smith KL, Wong J, Abrams M, Lytle M, et al. (2001) Francisella tularensis strain typing using multiple-locus, variable-number tandem repeat analysis. Journal of clinical microbiology 39: 3186.
34. Johansson A, Goransson I, Larsson P, Sjostedt A, (2001) Extensive allelic variation among Francisella tularensis strains in a short-sequence tandem repeat region. Journal of clinical microbiology 39: 3140.
35. Johansson A, Farlow J, Larsson P, Dukerich M, Chambers E, et al. (2004) Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. Journal of bacteriology 186: 5808-5818.
36. Achtman M, Zurth K, Morelli G, Torrea G, Guiyoule A, et al. (1999) Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proceedings of the National Academy of Sciences 96: 14043.
37. Achtman M, Morelli G, Zhu P, Wirth T, Diehl I, et al. (2004) Microevolution and history of the plague bacillus, Yersinia pestis. Proceedings of the National Academy of Sciences of the United States of America 101: 17837.
38. Trebesius K, Harmsen D, Rakin A, Schmelz J, Heesemann J, (1998) Development of rRNA-Targeted PCR and In Situ Hybridization with Fluorescently Labelled Oligonucleotides for Detection of Yersinia Species. Journal of Clinical Microbiology 36: 2557-2564.
39. Adair D, Worsham P, Hill K, Klevytska A, Jackson P, et al. (2000) Diversity in a variable-number tandem repeat from Yersinia pestis. Journal of clinical microbiology 38: 1516.
40. Girard JM, Wagner DM, Vogler AJ, Keys C, Allender CJ, et al. (2004) Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales. Proceedings of the National Academy of Sciences of the United States of America 101: 8408.
41. Drancourt M, Roux V, Vu Dang L, Tran-Hung L, Castex D, et al. (2004) Genotyping, Orientalis-like Yersinia pestis, and plague pandemics. Emerging infectious diseases 10: 1585-1592.
42. Motin VL, Georgescu AM, Elliott JM, Hu P, Worsham PL, et al. (2002) Genetic variability of Yersinia pestis isolates as predicted by PCR-based IS100 genotyping and analysis of structural genes encoding glycerol-3-phosphate dehydrogenase (glpD). Journal of bacteriology 184: 1019.
43. Pannucci J, Okinaka RT, Sabin R, Kuske CR, (2002) Bacillus anthracis pXO1 plasmid sequence conservation among closely related bacterial species. Journal of bacteriology 184: 134.
44. Pannucci J, Okinaka R, Williams E, Sabin R, Ticknor L, et al. (2002) DNA sequence conservation between the Bacillus anthracis pXO2 plasmid and genomic sequence from closely related bacteria. BMC genomics 3: 34.
45. Hoffmaster AR, Ravel J, Rasko DA, Chapman GD, Chute MD, et al. (2004) Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc Natl Acad Sci U S A 101: 8449-8454.
46. Klee SR, Brzuszkiewicz EB, Nattermann H, Bruggemann H, Dupke S, et al. (2010) The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids. PLoS One 5: e10986.
47. Rasko DA, Altherr MR, Han CS, Ravel J, (2005) Genomics of the Bacillus cereus group of organisms. FEMS microbiology reviews 29: 303-329.
48. Green B, Battisti L, Koehler T, Thorne C, Ivins B, (1985) Demonstration of a capsule plasmid in Bacillus anthracis. Infection and immunity 49: 291-297.
49. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, et al. (2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423: 81-86.
50. CDC.gov, Centers for Disease Control and Prevention. Anthrax Sterne strain (34F2) of Bacillus anthracis. National Center for Emerging and Zoonotic Infectious Diseases CDC. Available: http://www.cdc.gov/nczved/divisions/dfbmd/diseases/anthrax_sterne/. Accessed 2012 Oct.
51. Page R, Division of Ecology and Evolutionary Biology. Available: http://taxonomy.zoology.gla.ac.uk/rod/rod/html. Accessed 2012 Apr.
52. Ludu JS, de Bruin OM, Duplantis BN, Schmerk CL, Chou AY, et al. (2008) The Francisella pathogenicity island protein PdpD is required for full virulence and associates with homologues of the type VI secretion system. J Bacteriol. 4584-4595.
53. Pandya G, Holmes M, Petersen J, Pradhan S, Karamycheva S, et al. (2009) Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay. BMC microbiology 9: 213.
54. Huang XZ, Nikolich MP, Lindler LE, (2006) Current trends in plague research: from genomics to virulence. Clinical medicine & research 4: 189-199.
55. Bhaduri S, Sommers CH, (2008) Detection of Yersinia Pestis by Comparison of Virulence Plasmid (PYV/PCD) and Associated Phenotypes in Yersinia Species. Journal of Food Safety 28: 453-466.
56. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nature biotechnology 26: 1135-1145.
57. Voelkerding KV, Dames SA, Durtschi JD, (2009) Next-generation sequencing: from basic research to diagnostics. Clinical chemistry 55: 641-658.
58. Stapley J, Reger J, Feulner PGD, Smadja C, Galindo J, et al. (2010) Adaptation genomics: the next generation. Trends in Ecology & Evolution 25: 705-712.
59. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of molecular biology 215: 403-410.
60. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947.
61. Read TD, Turingan RS, Cook C, Giese H, Thomann UH, et al. (2010) Rapid multi-locus sequence typing using microfluidic biochips. PLoS One 5: e10595.