Computer-Intensive Statistical Procedures

The overall goal of this review is to summarize the current body of knowledge about the structure and function of major proteins of Bacillus anthracis and/or similar spore-forming organisms. B. anthracis is a key spore-forming biological threat agent, as well as human and animal Gram-positive bacterial pathogen. The structural information described here is limited to approximately the last 5 years. This information is then related to the role of the selected proteins in pathogenesis and in the possible development of novel vaccine and/or other antimicrobial agents against spore-forming organisms, including anthrax, a disease caused by B. anthracis.

Among spore-forming bacteria, Bacillus and Clostridium species are the predominant spore-forming bacilli that cause serious diseases. The biochemical properties and mechanism of catalysis of the novel spore germination protease that degrades small, acid-soluble proteins protecting DNA against damage, a cofactor independent phosphoglycerate mutase, NAD⁺ synthetase, and the three know B. anthracis toxins, protective antigen, lethal factor, and edema factor are described. The studies described in this work review and unify selected information critical for the prevention of microbial diseases such as anthrax. A strategy for the structure-guided development of new prophylactic and therapeutic agents is discussed.     

重要生物恐怖病原及其医学防护对策

生物恐怖问题由来已久,但直到美国“9.11”事件后的炭疽芽孢袭击才引起人们广泛关注。生物恐怖已成为21世纪全人类的威胁,防范生物恐怖病原袭击已成为各国政府的当务之急。本文主要介绍了对生物恐怖的定义、生物恐怖病原种类和致病特征,以及医学防护对策。     

Medical control of bioterrorism

Against the recently accrued risk of bioterrorism, the Biotox plan has been set up in order to take in charge any person that could be facing a potential terrorist contamination. It has to take into consideration the components of bioterrorism, i.e. the incubation period, the function of bacterial or viral agents, the variable number of concerned people, the difficulty of alert launching, and the diagnosis of the responsible agent. This plan relies on hospitals comprising departments of infectious diseases. Those are specifically in charge of informing, organising, and coordinating the reception of people having been in contact or infected by infectious agents, in order to isolate and treat them properly. The recent experience has allowed to test this plan, to precise and correct some of its features.     

Differential identification of Bacillus anthracis from environmental Bacillus species using microarray analysis

AIMS: To determine whether microarray analysis could be employed for the differential identification of a range of environmental Bacillus sp. from four strains of Bacillus anthracis. METHODS AND RESULTS: Oligonucleotide probes were designed that were specific to virulence factor genes of B. anthracis (pag, lef and cap), the variable number tandem repeat region of the B. anthracis vrrA gene and to the 16S-23S rRNA intergenic transcribed spacer region (ITS) and pleiotropic regulator (plcR) regions of the Bacillus cereus subgroup species. Generic probes were also designed to hybridize with conserved regions of the 16S rRNA genes of Bacillus (as a positive control), Neisseria sp., Pseudomonas sp., Streptococcus sp., Mycobacterium sp. and to all members of the Enterobacteriaceae to allow simultaneous detection of these bacteria. Identification of B. anthracis was found to rely entirely on hybridization of DNA specific to regions of the pag, lef and cap genes. Cross-reaction was observed between B. anthracis and other Bacillus species with all the other Bacillus probes tested. Results obtained using microarray hybridizations were confirmed using conventional microbiological techniques and found to have very high comparability. CONCLUSIONS: Microarray-based assays are an effective method for the identification of B. anthracis from mixed-culture environmental samples without problems of false-positivity that have been observed with conventional PCR assays. SIGNIFICANCE AND IMPACT OF THE STUDY: Identification of environmental Bacillus sp. by conventional PCR is prone to potential for reporting false-positives. This study provides a method for the exclusion of such isolates.     

Using Fault Tree Analysis to Assess Bioterrorist Risks to the U.S. Food Supply

Concerns about terrorist use of biological agents have increased at state and federal levels and in the popular press. Vulnerability of U.S. agricultural assets to bioterrorism has received less attention. A bioterrorist could use the U.S. food supply system to deliver a bioagent to a human target or use a bioagent to destroy it's inputs or infrastructure. Establishing effective agriculture security programs requires condensing generalizations about such bioterrorist threats into specific attack scenarios. This paper suggests a two-stage process to achieve this: problem formulation to define and rank scenarios, then quantitative risk assessment of selected, more highly ranked, scenarios. The quantitative component is illustrated for two specific scenarios: the actual 1984 Rajneeshee incident in Oregon and a hypothetical release of oral anthrax into the food supply system. The fault tree analysis of these scenarios suggests that the food supply system may be a less than optimal bioagent delivery mechanism, particularly if the objective is a mass casualty attack, as a number of events must occur simultaneously with reasonable probability if a bioagent is likely to be deployed effectively. In addition, an environmentally stable bioagent would be required if only the food system were used to deliver it to human consumers, but early detection of an intentional release common bioagent may be difficult absent specific intelligence or “unusual” epidemiological circumstances.     

Comparison of five commercial DNA extraction kits for the recovery of Yersinia pestis DNA from bacterial suspensions and spiked environmental samples

Aim:  To evaluate commercial DNA extraction kits for their ability to isolate DNA from Yersinia pestis suspensions and spiked environmental samples.
Methods and Results:  Five commercially available DNA extraction kits were evaluated: the ChargeSwitch gDNA Mini Bacteria Kit, the IT 1-2-3 Sample DNA Purification Kit, the MasterPure Complete DNA and RNA Purification Kit, the QIAamp DNA Blood Mini Kit and the UltraClean Microbial DNA Isolation Kit. The extraction methods were performed upon six Y. pestis strains and spiked environmental specimens, including three swab types and one powder type. Taqman real-time PCR analysis revealed that the use of the MasterPure kit resulted in DNA with the most consistently positive results and the lowest limit of detection from Y. pestis suspensions and spiked environmental samples.
Conclusion:  Comparative evaluations of the five commercial DNA extraction methods indicated that the MasterPure kit was superior for the isolation of PCR-amplifiable DNA from Y. pestis suspensions and spiked environmental samples.
Significance and Impact of the Study:  The results of this study can assist diagnostic laboratories with selecting the best extraction method for processing environmental specimens for subsequent detection of Y. pestis by real-time PCR.     

城市小区环境生物剂气溶胶的扩散模拟研究

目的:研究城市小区中生物剂气溶胶的扩散模拟和污染区域的划分,为反生物恐怖危害评估及应急响应提供决策依据。方法:以典型生物剂炭疽为例,利用计算流体力学中的离散相模型对小区环境中生物剂气溶胶的扩散规律进行研究;对扩散后生物剂气溶胶的数目分布进行量化分析,结合吸入式炭疽的剂量-反应模型进行污染区域的划分。结果:通过计算机模拟,得到了生物剂气溶胶在小区环境中的扩散规律及数目分布,并依据人员感染炭疽概率的不同划分出小区内的污染区域。结论:利用离散相模型和剂量-反应模型,可以对城市小区中生物剂气溶胶的扩散规律进行模拟并划分污染区域,为反生物恐怖危害评估及应急响应提供决策依据。     

Comparative genomics tools applied to bioterrorism defence

Rapid advances in the genomic sequencing of bacteria and viruses over the past few years have made it possible to consider sequencing the genomes of all pathogens that affect humans and the crops and livestock upon which our lives depend. Recent events make it imperative that full genome sequencing be accomplished as soon as possible for pathogens that could be used as weapons of mass destruction or disruption. This sequence information must be exploited to provide rapid and accurate diagnostics to identify pathogens and distinguish them from harmless near-neighbours and hoaxes. The Chem-Bio Non-Proliferation (CBNP) programme of the US Department of Energy (DOE) began a large-scale effort of pathogen detection in early 2000 when it was announced that the DOE would be providing bio-security at the 2002 Winter Olympic Games in Salt Lake City, Utah. Our team at the Lawrence Livermore National Lab (LLNL) was given the task of developing reliable and validated assays for a number of the most likely bioterrorist agents. The short timeline led us to devise a novel system that utilised whole-genome comparison methods to rapidly focus on parts of the pathogen genomes that had a high probability of being unique. Assays developed with this approach have been validated by the Centers for Disease Control (CDC). They were used at the 2002 Winter Olympics, have entered the public health system, and have been in continual use for non-publicised aspects of homeland defence since autumn 2001. Assays have been developed for all major threat list agents for which adequate genomic sequence is available, as well as for other pathogens requested by various government agencies. Collaborations with comparative genomics algorithm developers have enabled our LLNL team to make major advances in pathogen detection, since many of the existing tools simply did not scale well enough to be of practical use for this application. It is hoped that a discussion of a real-life practical application of comparative genomics algorithms may help spur algorithm developers to tackle some of the many remaining problems that need to be addressed. Solutions to these problems will advance a wide range of biological disciplines, only one of which is pathogen detection. For example, exploration in evolution and phylogenetics, annotating gene coding regions, predicting and understanding gene function and regulation, and untangling gene networks all rely on tools for aligning multiple sequences, detecting gene rearrangements and duplications, and visualising genomic data. Two key problems currently needing improved solutions are: (1) aligning incomplete, fragmentary sequence (eg draft genome contigs or arbitrary genome regions) with both complete genomes and other fragmentary sequences; and (2) ordering, aligning and visualising non-colinear gene rearrangements and inversions in addition to the colinear alignments handled by current tools.     

Bacillus anthracis contamination and inhalational anthrax in a mail processing and distribution center

AIMS: Four inhalational anthrax cases occurred in a large mail processing and distribution center in Washington, DC, after envelopes containing Bacillus anthracis spores were processed. This report describes the results of sampling for B. anthracis spores during investigations conducted in October and December 2001. METHODS AND RESULTS: Wet swabs, wet wipes, vacuum sock, and air-filter samples were collected throughout the facility to characterize the extent of building contamination. The results showed widespread contamination of B. anthracis spores, particularly associated with one delivery bar code sorter (DBCS) machine that had sorted the spore-containing envelopes and an area where the envelopes were handled by postal workers. Spore concentrations decreased as distance from the DBCS machine increased, but spores were widely dispersed into surrounding areas. CONCLUSION: The spatial distribution of culture positive samples was closely related to the work areas of the inhalational anthrax cases and supported epidemiological evidence that the workers became ill from exposure to B. anthracis spores in areas where the contaminated envelopes had travelled. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this investigation were used to guide decontamination efforts and provided baseline spore concentrations for follow-up measurements after the building had been cleaned. Implementing methods to reduce aerosolization and dispersion of dust within the facility would reduce postal workers' potential exposures to bioterrorism agents.