Identification of Bacillus and Yersinia species and hoax agents by protein profiling using microfluidic capillary electrophoresis with peak detection algorithms

References

• Nelson M, Roffey P, McNevin D, Lennard C, Gahan ME. An overview of biosecurity in Australia. Aust J Forensic Sci. 2014;46:383–396. doi:10.1080/00450618.2014.882986
   Web of Science ®Google Scholar
• Duncan A. Biological weapons and bioterrorism. Chem Aust. 2005;72:5–6.
   Google Scholar
• Ligon BL. Plague: a review of its history and potential as a biological weapon. Semin Pediatr Infect Dis. 2006;17:161–170. doi:10.1053/j.spid.2006.07.002
   Google Scholar
• Bossi P, Garin D, Guihot A, Gay F, Crance JM, Debord T, Autran B, Bricaire F. Bioterrorism: management of major biological agents. Cell Mol Life Sci. 2006;63:2196–2212. doi:10.1007/s00018-006-6308-z
   PubMed Web of Science ®Google Scholar
• Bush LM, Abrams BH, Beall A, Johnson CC. Index case of fatal inhalational anthrax due to bioterrorism in the United States. N Engl J Med. 2001;345:1607–1610. doi:10.1056/NEJMoa012948
   PubMed Web of Science ®Google Scholar
• Morse SA, Kellogg RB, Perry S, Meyer RF, Bray DA, Nichelson D, Miller JM. Detecting biothreat agents: the laboratory response network. ASM News. 2003;69:433–437.
   Google Scholar
• Franz DR. Preparedness for an anthrax attack. Mol Aspects Med. 2009;30:503–510. doi:10.1016/j.mam.2009.07.002
   PubMed Web of Science ®Google Scholar
• Rao SS, Mohan KVK, Atreya CD. Detection technologies for Bacillus anthracis: prospects and challenges. J Microbiol Methods. 2010;82:1–10. doi:10.1016/j.mimet.2010.07.004
   PubMed Web of Science ®Google Scholar
• Takahashi H, Keim P, Kaufmann AF, Keys C, Smith KL, Taniguchi K, Inouye S, Kurata T. Bacillus anthracis incident, Kameido, Tokyo, 1993. Emerg Infect Dis. 2004;10:117–120. doi:10.3201/eid1001.030238
   PubMed Web of Science ®Google Scholar
• Jesmok EM, Hopkins JM, Foran DR. Next-generation sequencing of the bacterial 16S rRNA gene for forensic soil comparison: a feasibility study. J Forensic Sci. 2016;61:607–617. doi:10.1111/1556-4029.13049
   PubMed Web of Science ®Google Scholar
• Be NA, Thissen JB, Gardner SN, McLoughlin KS, Fofanov VY, Koshinsky H, Ellingson SR, Brettin TS, Jackson PJ, Jaing CJ. Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing. PLoS One. 2013;8:e73455. doi:10.1371/journal.pone.0073455
   PubMed Web of Science ®Google Scholar
• Gahan ME, Bowman S, Chevalier R, Rossi R, Nelson M, Roffey P, Xu B, Power D, McNevin D. Bacillus species at the Canberra Airport: A comparison of real-time polymerase chain reaction and massively parallel seqeuencing for identification. Forensic Sci Int. 2019;295:169–178. doi:10.1016/j.forsciint.2018.12.011
   PubMed Web of Science ®Google Scholar
• Vogler AJ, Keim P, Wagner DM. A review of methods for subtyping Yersinia pestis: from phenotypes to whole genome sequencing. Infect Genet Evol. 2016;37:21–36. doi:10.1016/j.meegid.2015.11.006
   PubMed Web of Science ®Google Scholar
• Herzog AB, McLennan SD, Pandey AK, Gerba CP, Haas CN, Rose JB, Hashsham SA. Implications of limits of detection of various methods for Bacillus anthracis in computing risks to human health. Appl Environ Microbiol. 2009;75:6331–6339. doi:10.1128/AEM.00288-09
   PubMed Web of Science ®Google Scholar
• Irenge LM, Gala JL. Rapid detection methods for Bacillus anthracis in environmental samples: a review. Appl Microbiol Biotechnol. 2012;93:1411–1422. doi:10.1007/s00253-011-3845-7
   PubMed Web of Science ®Google Scholar
• Hutchison JR, Erikson RL, Sheen AM, Ozanich RM, Kelly RT. Reagent-free and portable detection of Bacillus anthracis spores using a microfluidic incubator and smartphone microscope. Analyst. 2015;140:6269–6276. doi:10.1039/C5AN01304F
   PubMed Web of Science ®Google Scholar
• Pizarro SA, Lane P, Lane TW, Cruz E, Haroldsen B, VanderNoot VA. Bacterial characterization using protein profiling in a microchip separations platform. Electrophoresis. 2007;28:4697–4704. doi:10.1002/(ISSN)1522-2683
   PubMed Web of Science ®Google Scholar
• Stachowiak JC, Shugard EE, Mosier BP, Renzi RF, Caton PF, Ferko SM, Van de Vreugde JL, Yee DD, Haroldsen BL, VanderNoot VA. Autonomous microfluidic sample preparation system for protein profile-based detection of aerosolized bacterial cells and spores. Anal Chem. 2007;79:5763–5770. doi:10.1021/ac070567z
   PubMed Web of Science ®Google Scholar
• McLaughlin J, Nelson M, McNevin D, Roffey P, Gahan ME. Characterization of Bacillus strains and hoax agents by protein profiling using automated microfluidic capillary electrophoresis. Forensic Sci Med Pathol. 2014;10:380–389. doi:10.1007/s12024-014-9578-z
   PubMed Web of Science ®Google Scholar
• Bennett V, McNevin D, Roffey P, Gahan ME. Characterization of Yersinia strains by protein profiling using automated microfluidic capillary electrophoresis. Forensic Sci Med Pathol. 2017;13:10–19. doi:10.1007/s12024-016-9824-7
   PubMed Web of Science ®Google Scholar
• Li X. PROcess: ciphergen SELDI-TOF processing. R package version 1.46.0. 2005. Available from: http://bioconductor.org/packages/PROcess/
   Google Scholar
• Yang C, He Z, Yu W. Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis. BMC Bioinformatics. 2009;10:1–13. doi:10.1186/1471-2105-10-4
   PubMed Web of Science ®Google Scholar
• Li X, Gentleman R, Lu X, Shi Q, Iglehart JD, Harris L, Miron A. SELDI-TOF mass spectrometry protein data. In: Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S, editors. Bioinformatics and computational biology solutions using R and bioconductor. New York: Springer; 2005. p. 91–109.
   Google Scholar
• Cruz-Marcelo A, Guerra R, Vannucci M, Li Y, Lau CC, Man T. Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data. Bioinformatics. 2008;24:2129–2136. doi:10.1093/bioinformatics/btn398
   PubMed Web of Science ®Google Scholar
• Wu LC, Chen HH, Horng JT, Lin C, Huang NE, Cheng YC, Cheng KF. A novel preprocessing method using Hilbert Huang transform for MALDI-TOF and SELDI-TOF mass spectrometry data. PLoS One. 2010;5:e12493. doi:10.1371/journal.pone.0012493
   PubMed Web of Science ®Google Scholar
• Kauffman SA. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol. 1969;22:437–467. doi:10.1016/0022-5193(69)90015-0
   PubMed Web of Science ®Google Scholar
• Kauffman SA. The origins of order: self-organization and selection in evolution. New York: Oxford University Press; 1993.
   Google Scholar
• Aldana M, Coppersmith S, Kadanoff LP. Boolean dynamics with random couplings. In: Kaplan E, Marsden JE, Sreenivasan KR, editors. Perspectives and problems in nonlinear science. New York: Springer; 2002. p. 23–89.
   Google Scholar
• Shmulevich I, Kauffman SA. Activities and sensitivities in Boolean network models. Phys Rev Lett. 2002;93:e048701.
   Web of Science ®Google Scholar
• Shmulevich I, Dougherty ER, Kim S, Zhang W. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics. 2002;18:261–274. doi:10.1093/bioinformatics/18.2.261
   PubMed Web of Science ®Google Scholar
• R Core Team. R: A language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing; 2016. Available from: https://www.R-project.org/
   Google Scholar
• Walker A. Openxlsx: read, write and edit XLSX files. R package version 3.0.0. 2015. Available from: https://CRAN.R-project.org/package=openxlsx
   Google Scholar
• Wickham H. Stringr: simple, consistent wrappers for common string operations. R package version 1.0.0. 2015. Available from: https://CRAN.R-project.org/package=stringr
   Google Scholar
• Wickham H. Reshaping data with the reshape package. J Stat Softw. 2007;21:1–20. Available from: http://www.jstatsoft.org/v21/i12/ doi:10.18637/jss.v021.i12
   Web of Science ®Google Scholar
• Norman K, Roffey P, Royds D. Application of a mobile laboratory for real time response to incidents. Aust J Forensic Sci. 2009;41:73–80. doi:10.1080/00450610802452236
   Web of Science ®Google Scholar
• Helgason E, Økstad OA, Caugant DA, Johansen HA, Fouet A, Mock M, Hegna I, Kolstø AB. Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis—one species on the basis of genetic evidence. Appl Environ Microbiol. 2000;66:2627–2630. doi:10.1128/AEM.66.6.2627-2630.2000
   PubMed Web of Science ®Google Scholar
• Han CS, Xie G, Challacombe JF, Altherr MR, Bhotika SS, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O, et al. Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis. J Bacteriol. 2006;188:3382–3390. doi:10.1128/JB.00698-06
   PubMed Web of Science ®Google Scholar
• Marston CK, Gee JE, Popovic T, Hoffmaster AR. Molecular approaches to identify and differentiate Bacillus anthracis from phenotypically similar Bacillus species isolates. BMC Microbiol. 2006;6:1–7. doi:10.1186/1471-2180-6-42
   PubMed Web of Science ®Google Scholar