Composition of bacillus species in aerosols from 11 U.S. cities

A PCR-based heteroduplex assay was used to determine the presence and composition of Bacillus species in 11,059 Environmental Protection Agency PM2.5 aerosol samples from 11 U.S. cities. The assay differentiated three groups: Type A containing Bacillus anthracis and very closely related, often pathogenic, Bacillus cereus and Bacillus thuringiensis strains; Type B containing other B. cereus and B. thuringiensis strains; and a third group of more-distantly related Bacillus species. Eight of the 11 cities were positive for Bacillus species in 50% or more of the samples, and the percent of aerosol samples that contained the HD Type A group ranged from 3% to 32%. Cities from the eastern half of the United States generally contained a higher frequency and broader diversity of Bacillus species than the western half of the United States. Positive samples were detected throughout the year. These results have implications for pathogen detection in environmental samples, understanding the natural evolution of new pathogenic strains, and incidence of infection caused by strains of the B. cereus subgroup.     

Environmental survey for four pathogenic bacteria and closely related species using phylogenetic and functional genes

Bacterial species with high DNA sequence similarity to pathogens could affect the specificity of assays designed to detect biological threat agents in environmental samples. The natural presence of four pathogenic bacteria, Bacillus anthracis, Clostridium perfringens, Francisella tularensis, and Yersinia pestis and their closely related species, was determined for a large collection of soil and aerosol samples. Polymerase chain reaction (PCR) and gene sequencing were used using group-specific 16S rRNA primers to identify pathogens and related species, and pathogen-specific virulence genes. Close relatives of B. anthracis (B. cereus group species) were detected in 37% of the soils and 25% of the aerosol samples. The B. anthracis protective antigen (pag) gene or a close homolog was detected in 16 of these samples. For the other three pathogen groups, the frequency of detection was much lower, and none of the samples were positive with both the phylogenetic and virulence gene primer sets.     

Trace detection of meglumine and diatrizoate from Bacillus spore samples using liquid chromatography/mass spectrometry

Following the September 11, 2001 terrorist attacks, letters containing Bacillus anthracis were distributed through the United States postal system killing five people. A complex forensic investigation commenced to identify the perpetrator of these mailings. A novel liquid chromatography/mass spectrometry protocol for the qualitative detection of trace levels of meglumine and diatrizoate in dried spore preparations of B. anthracis was developed. Meglumine and diatrizoate are components of radiographic imaging products that have been used to purify bacterial spores. Two separate chromatographic assays using multiple mass spectrometric analyses were developed for the detection of meglumine and diatrizoate. The assays achieved limits of detection for meglumine and diatrizoate of 1.00 and 10.0 ng/mL, respectively. Bacillus cereus T strain spores were effectively used as a surrogate for B. anthracis spores during method development and validation. This protocol was successfully applied to limited evidentiary B. anthracis spore material, providing probative information to the investigators.     

Comparison of quantitative PCR and culture-based methods for evaluating dispersal of Bacillus thuringiensis endospores at a bioterrorism hoax crime scene

Since the anthrax mail attacks of 2001, law enforcement agencies have processed thousands of suspicious mail incidents globally, many of which are hoax bioterrorism threats. Bio-insecticide preparations containing Bacillus thuringiensis (Bt) spores have been involved in several such threats in Australia, leading to the requirement for rapid and sensitive detection techniques for this organism, a close relative of Bacillus anthracis. Here we describe the development of a quantitative PCR (qPCR) method for the detection of Bt crystal toxin gene cry1, and evaluation of the method's effectiveness during a hoax bioterrorism event in 2009. When combined with moist wipe sampling, the cry1 qPCR was a rapid, reliable, and sensitive diagnostic tool for detecting and quantifying Bt contamination, and mapping endospore dispersal within a mail sorting facility. Results from the cry1 qPCR were validated by viable counts of the same samples on Bacillus-selective agar (PEMBA), which revealed a similar pattern of contamination. Extensive and persistent contamination of the facility was detected, both within the affected mailroom, and extending into office areas up to 30m distant from the source event, emphasising the need for improved containment procedures for suspicious mail items, both during and post-event. The cry1 qPCR enables detection of both viable and non-viable Bt spores and cells, which is important for historical crime scenes or scenes subjected to decontamination. This work provides a new rapid method to add to the forensics toolbox for crime scenes suspected to be contaminated with biological agents.     

Effect of Sterilants on Amplification and Detection of Target DNA from Bacillus cereus Spores

To conceal criminal activity of a bioterrorist or agroterrorist, the site of pathogen generation is often treated with sterilants to kill the organisms and remove evidence. As dead organisms cannot be analyzed by culture, this study examined whether DNA from sterilant‐treated Bacillus cereus spores was viable for amplification. The spores were exposed to five common sterilants: bleach, Sterilox®, oxidizer foam (L‐Gel), a peroxyacid (Actril®), and formaldehyde vapor. The spores were inoculated on typical surfaces found in offices and laboratories to test for environmental effects. It was found that the surface influenced the efficiency of recovery of the organisms. The DNA isolated from the recovered spores was successfully detected using RT‐qPCR for all treatments except for formaldehyde, by amplifying the phosphatidylinositol phospholipase C and sphingomyelinase genes. The results demonstrated that evidence from sites treated with sterilants can still provide information on the uncultured organism, using DNA amplification.     

Bioterrorism: processing contaminated evidence, the effects of formaldehyde gas on the recovery of latent fingermarks

In the present age of heightened emphasis on counter terrorism, law enforcement and forensic science are constantly evolving and adapting to the motivations and capabilities of terrorist groups and individuals. The use of biological agents on a population, such as anthrax spores, presents unique challenges to the forensic investigator, and the processing of contaminated evidence. In this research, a number of porous and nonporous items were contaminated with viable anthrax spores and marked with latent fingermarks. The test samples were then subjected to a standard formulation of formaldehyde gas. Latent fingermarks were then recovered post decontamination using a range of methods. Standard fumigation, while effective at destroying viable spores, contributed to the degradation of amino acids leading to loss of ridge detail. A new protocol for formaldehyde gas decontamination was developed which allows for the destruction of viable spores and the successful recovery of latent marks, all within a rapid response time of less than 1 h.     

Application of the hexagon-OBTI test and the RSID blood test for the determination of the post-mortem interval of bone samples

In this serial experiment, five human bones with known post-mortem intervals (PMI) in a soil environment from five different epochs (0.2 to approximately 2000 years) were tested in a blind setup with two established rapid tests for the identification of human blood traces (Hexagon-OBTI test and RSID blood test). Based on previous study results concerning the usability of the Luminol test for the first assessment of the PMI of osseous remains, the question arising was whether those test procedures, which are highly sensitive for the detection of human blood components, could also be used to narrow down the post-mortem interval. Five test series were conducted applying modified standard protocols of the manufactures. The aim was to find out whether with prior reaction steps or a prolonged time of incubation hemoglobin or its metabolites can be dissolved from the bone and positive test results can be achieved dependent on the PMI. Four test series yielded negative results for all bone samples and one test series a uniformly weak positive result. The results indicate that rapid tests based on the detection of blood are not suitable for the determination of the PMI of bone samples despite the modification of the standard protocols. Further thorough research is required to clarify the postmortem degradation of hemoglobin in bones.     

To destroy snail mail: Is this the sole solution for anthrax contaminated letters?

Suspicious packages, strange addresses on envelopes and/or the presence of particular powders: these are the most popular aspects of letters containing Bacillus anthracis. Since the World Trade Center tragedy, alarmism about chemical or biological attacks is always in force. The Italian Ministry of Foreign Affairs introduced new procedures to be followed in case suspected anthrax letters are identified (Ministry of Health PROT. 400.3/120.33/4786 of 23/10/2001). Scientists have to collect samples from surfaces and infectious waste have to be placed in autoclavable bags for decontamination. After the sterilization, mails and packages are burnt thus eliminating every biological trace present on their surface. As a matter of fact, after sterilization, DNA is still present and can be analyzed for forensic purposes: for this reason, here we report on the importance of preserving sterilized substrates. We recreated false infected mails with biological traces on their surfaces, sterilized them and, subsequently, we took samples of biological stains and processed them for DNA quantification and typing. We recreate different time conditions consistent with those of the postal service too. Real-Time PCR and DNA typing showed that, even if sterilization destroys the bacillus, human genomic traces still persist and we obtained both complete and partial profiles of samples’ donors. To conclude, the problem of anthrax contaminated letter call for peculiar and standardized procedures; nonetheless, we show that burning evidences after the sterilization process does not appear to be the best solution since there is a loss of biological material which could be decisive for forensic purposes.     

Potential and pitfalls in establishing the provenance of Earth-related samples in forensic investigations

Earth scientists are often asked to establish or constrain the likely provenance of very small quantities of earth-related material as part of a forensic investigation. We tested the independent and collective interpretations of four experts with differing analytical skills in the prediction of sample provenance for three samples from different environmental settings. The methods used were X-ray diffraction, scanning electron microscopy, the assessment of pollen assemblages, and structural characterization of organic matter at the molecular level. Independent interpretations were less accurate than those where multiple techniques were combined. Collective interpretation was very effective in the assessment of provenance for two of the three sites where the mineralogy and plant communities were distinctive. At the other site, although the mineralogical analysis correctly identified the Triassic mudstone soil parent material, Carboniferous spores from domestic coal were initially interpreted as deriving directly from bedrock. Such an interpretation could be a common pitfall owing to anthropogenic redistribution of material such as coal.     

Validation of the barcoding gene COI for use in forensic genetic species identification

The application of forensics to wildlife crime investigation routinely involves genetic species identification based on DNA sequence similarity. This work can be hindered by a lack of authenticated reference DNA sequence data resulting in weak matches between evidence and reference samples. The introduction of DNA barcoding has highlighted the expanding use of the mtDNA gene, cytochrome c oxidase I (COI), as a genetic marker for species identification. Here, we assess the COI gene for use in forensic analysis following published human validation guidelines. Validation experiments investigated reproducibility, heteroplasmy, mixed DNA, DNA template concentration, chemical treatments, substrate variation, environmental conditions and thermocycling parameters. Sequence similarity searches using both GenBank BLASTn and BOLD search engines indicated that the COI gene consistently identifies species where authenticated reference sequence data exists. Where misidentification occurred the cause was attributable to either erroneous reference sequences from published data, or lack of primer specificity. Although amplification failure was observed under certain sample treatments, there was no evidence of environmentally induced sequence mutation in those sequences that were generated. A simulated case study compared the performance of COI and cytochrome b mtDNA genes. Findings are discussed in relation to the utility of the COI gene in forensic species identification.     

胶体金标记苯丙胺单克隆抗体免疫试剂盒研究

目的建立一种准确、快速、简便的检测尿液中苯丙胺(AMP)的胶体金免疫层析技术。方法采用柠檬酸三钠还原法制备胶体金颗粒,标记抗AMP单抗,将AMP—BSA抗原固相于硝酸纤维素膜上,制备胶体金免疫层析测试条。通过尿液、血液和唾液中的可能存在的苯丙胺成分与测试条上的苯丙胺-BSA完全抗原竞争结合有限的单抗结合位点,来判定检测结果。结果用ICT法和GC/MS检测217份尿样,本法检测阈值为1000ng/mL,特异性为99.17%,准确性为99.54%。结论ICT法检测尿液中的AMP特异性强,灵敏度高、简便快速、无需特殊仪器设备,具有广泛应用价值。     

Evaluation of DNA Extraction Methods for Processing Fingerprint Powder-Coated Forensic Evidence

In unison, fingerprinting and DNA analysis have played a pivotal role in forensic investigations. Fingerprint powders that are available on the market can come in a range of colors and with specific properties. This study evaluated the efficiency of DNA extraction from samples coated with 3 brands of fingerprint powders: Lightning, Sirchie, and SupraNano, covering a range of colors and properties. A total of 23 fingerprint powders were tested using the Chelex, Promega DNA IQ™, and Applied Biosystems™ PrepFiler™ DNA extraction protocols. The DNA IQ™ and PrepFiler™ methods extracted higher yields of DNA in comparison to Chelex, which also accounted for better quality of PowerPlex x00AE; 21 DNA profiles recovered. There were no signs of degradation or inhibition in the quantification data, indicating that samples returning low DNA yield was due to interference during DNA extraction and not PCR inhibition. DNA profiles were recovered from the majority of fingerprint powders with only a single powder, Sirchie Magnetic Silver, failing to produce a profile using any of the methods tested. A link was observed between the DNA extraction chemistry, fingerprint powder property, that is, nonmagnetic, magnetic and aqueous, and the brand of fingerprint powder. Overall, the DNA IQ™ method was favorable for nonmagnetic fingerprint powders, while magnetic fingerprint powders produced more DNA profiles when extracted with the PrepFiler™ chemistry. This study highlights the importance of screening DNA extraction chemistries for the type of fingerprint powder used, as there is not a single DNA extraction method that suits all fingerprint powder brands and properties.     

氯胺酮胶体金标记单克隆抗体免疫层析检测板的研制

目的建立一种简便快速检测氯胺酮的方法。方法将20nm胶体金颗粒标记的抗氯胺酮单克隆抗体,均匀浸在吸水玻璃纤维上,用点膜机将氯胺酮-BSA和纯化后的羊抗鼠IgG多克隆抗体在硝酸纤维薄膜分别划1mm宽的检测线(T线)和质控线(C线),然后依次将吸水玻璃纤维、硝酸纤维薄膜和吸水滤纸粘贴于白色的塑料片上,切成0.5 cm×10 cm大小,制成氯胺酮胶体金标记单克隆抗体免疫层析检测条,并组装成检测板,并检测其特异性和灵敏度。结果氯胺酮胶体金标记单克隆抗体免疫层析检测板在对46种药(毒)物的测试中,仅识别氯胺酮及其主要代谢产物,其准确性为97.6%,检测氯胺酮的阈值为1000ng/m l。结论氯胺酮胶体金标记单克隆抗体免疫层析检测板在5m in内可检出样品中的氯胺酮及其代谢物。     

可卡因及其代谢物苯甲酰爱康宁胶体金检测试剂盒的研制

目的根据胶体金免疫层析的原理,建立一种可以在现场快速检测可卡因及其代谢物苯甲酰爱康宁的方法。方法将胶体金标记的抗可卡因单克隆抗体均匀浸涂在玻璃纤维膜上,用点膜仪将可卡因的完全抗原以及羊抗鼠多抗在硝酸纤维素膜上划线,分别作为可卡因的检测区（T）和质控区（C）。并且对样品垫用0.2%Tween 20和0.5%PVA封闭处理。样本（尿样、唾液、血样等）中游离的可卡因及其代谢物同包被的完全抗原分别免疫竞争结合胶体金标记的抗可卡因单抗。肉眼观察试剂盒的质控区和检测区上有无紫红色带来判读结果。结果可卡因胶体金检测试剂盒对65种毒品、药物的特异性测试中仅识别可卡因及其代谢物。对人体尿样中的可卡因和苯甲酰爱康宁检测阈值均为300ng/mL。与GC/MS对照试验,其准确性分别为98.9%和98.6%。在常温下能稳定保存2年。结论该可卡因检测试剂盒在5min内可以检测出样本中的可卡因及其代谢物成分。     

检测丁丙诺啡的胶体金标记单克隆抗体免疫试剂盒研制

目的采用免疫竞争法原理,建立一种简便快速检测丁丙诺啡的方法。方法将20nm胶体金颗粒标记的抗丁丙诺啡单克隆抗体,均匀浸在吸水玻璃纤维上,将丁丙诺啡-BSA和纯化后的羊抗鼠IgG多克隆抗体在硝酸纤维薄膜分别划1mm宽的检测线(T线)和质控线(C线),制成丁丙诺啡胶体金标记单克隆抗体免疫层析检测条,并组装成检测板。结果以GC/MS为标准对照,100例样品检测结果显示,本检测板的准确率为99.0%。丁丙诺啡胶体金标记单克隆抗体免疫层析检测板在对45种药(毒)物的测试中,仅识别丁丙诺啡及其主要代谢产物。结论丁丙诺啡胶体金标记单克隆抗体免疫层析检测板在5min内可检出样品中的丁丙诺啡及其代谢物,检测丁丙诺啡的阈值为100ng/mL。     

Systematic approach to the profiling analysis of illicit amphetamine

The use of automated workstations for the study of the origin of illicit produced amphetamine was examined by comparing the precision of peak identification methods of gas chromatographically determined impurities of confiscated amphetamine powders. The identification parameters used were absolute and relative retention times and retention indices. The retention index monitoring proved to be the most precise identification method when intralaboratory repeatability was examined. Preprocessing of gas chromatographic data is needed when automating pattern recognition for rapid screening of the impurities of amphetamine powder. Normalisation of peak areas of the impurity components was studied; scaled data were calculated by dividing peak areas of the chromatogram by the peak area of a selected impurity component of the same chromatogram. The precision of the gas chromatographic method of analysis in a large impurity concentration range was determined by comparing both the normalisation and the quantitation method of analysis with each other. Normalisation was a more precise way to preprocess data than quantitation on the basis of relative standard deviation values for the comparison. In order to get chromatographic data quickly for pattern recognition it is appropriate to prepare amphetamine powders with the same moisture content before making the analysis. The method of drying powders was studied by comparing gas chromatographically produced results of analyses of powders dried at an ambient temperature to those dried using infra-red radiation. The infra-red drying method proved to be suitable for the rapid preparation and analysis of amphetamine powders.     

Particle size analysis of sediments, soils and related particulate materials for forensic purposes using laser granulometry

Particle size is a fundamental property of any sediment, soil or dust deposit which can provide important clues to nature and provenance. For forensic work, the particle size distribution of sometimes very small samples requires precise determination using a rapid and reliable method with a high resolution. The Coulter trade mark LS230 laser granulometer offers rapid and accurate sizing of particles in the range 0.04-2000 microm for a variety of sample types, including soils, unconsolidated sediments, dusts, powders and other particulate materials. Reliable results are possible for sample weights of just 50 mg. Discrimination between samples is performed on the basis of the shape of the particle size curves and statistical measures of the size distributions. In routine forensic work laser granulometry data can rarely be used in isolation and should be considered in combination with results from other techniques to reach an overall conclusion.     

Are these food products fraudulent? Rapid and novel triplex-direct PCR assay for meat identification

Unintentional contamination and fraudulent labeling of food, especially in halal-certified products, breach both religious and international laws. DNA-based methods are widely employed to identify trace amount of contaminants for law enforcement. Direct PCR has proved successful in the DNA analysis from degraded samples and PCR-inhibited samples, but it has never been applied to meat identification from food products. In this study, we aimed to develop a multiplex direct PCR assay for simultaneous identification of three commonly consumed meats without the need to extract DNA. Species-specific primers were designed from the mitochondrial DNA using the alignment of sequences available on GenBank. The assay was validated for its specificity, sensitivity, and usefulness in market sample analysis. The results showed that a highly specific and sensitive multiplex direct PCR assay was developed and provided the expected PCR fragment of approximately 100, 119, and 133 bp for pork (Sus scrofa), mutton (Ovis aries), and chicken (Gallus gallus), respectively. Thirty-nine market samples were tested and a small number of fraudulent labeling was detected. In conclusion, we developed a rapid and inexpensive test for three meat species. This cost- and time-saving assay could be easily adopted in the world food hubs, which are mostly third-world countries.     

Validation and implementation of the PowerPlex 16 BIO System STR multiplex for forensic casework

The PowerPlex 16 BIO multiplex short tandem repeat (STR) system contains the 13 CODIS loci (FGA, TPOX, D8S1179, vWA, D18S51, D21S11, TH01, D3S1358, CSF1PO, D16S539, D7S820, D13S317, and DS5S818), plus two pentanucleotide repeat loci (Penta D and Penta E) and the sex-identifying locus. Amelogenin. The PowerPlex 16 BIO System is optimized for use with the Hitachi FMBIO gel imaging systems. A consortium of seven independent laboratories collaborated to perform the studies defined by the FBI standards for performing a developmental validation, including the evaluation of sample concordance, percent stutter determination, nonprobative casework, precision, sensitivity, mixture determination, effect of substrates, the impact of environmental insults, and species specificity. All samples tested for concordance were consistent except for one sample from the Virginia Division of Forensic Science database that displayed discordance at D13S317, a locus whose primer sequence was altered. Stutter values were comparable to those of other STR multiplex systems, the precision was comparable to other multiplexes analyzed by gel electrophoresis, the DNA profiles were unchanged by the substrate upon which the blood samples were placed, and the nonprobative casework samples re-typed for the PowerPlex 16 BIO System were consistent with previous typing results. When greater than 0.125 ng of DNA was placed into the PowerPlex 16 BIO System amplification reaction, a full profile was generated by all laboratories. The mixture study results were comparable to those reported for other multiplex systems, the environmental study demonstrated a loss of larger molecular weight loci when samples were incubated at elevated temperatures for a prolonged period of time, and the only notable cross species hybridization was observed with primate DNA samples. This extensive validation work performed demonstrates that the PowerPlex 16 BIO System provides STR data of a quality comparable with other PowerPlex STR multiplex kits as well as other widely used STR multiplexes and is thus suitable for evidentiary casework analysis as well as database sample profiling.