Novel sample preparation method for safe and rapid detection of Bacillus anthracis spores in environmental powders and nasal swabs

Zirconium-Directed Supramolecular Self-Assembly of Coenzyme A@GNCs with Enhanced Phosphorescence for Developing Ultrasensitive Tracer Probe of Dipicolinic Acid, a Biomarker of Bacterial Spores

Luminescent gold nanoclusters (GNCs) are a class of attractive quantum-sized nanomaterials bridging the gap between organogold complexes and gold nanocrystals. They typically have a core-shell structure consisting of a Au(I)-organoligand shell-encapsulated few-atom Au(0) core. Their luminescent properties are greatly affected by their Au(I)-organoligand shell, which also supports the aggregation-induced emission (AIE) effect. However, so far, the luminescent Au nanoclusters encapsulated with the organoligands containing phosphoryl moiety have rarely been reported, not to mention their AIE. In this study, coenzyme A (CoA), an adenosine diphosphate (ADP) analogue that is composed of a bulky 5-phosphoribonucleotide adenosine moiety connected to a long branch of vitamin B5 (pantetheine) via a diphosphate ester linkage and ubiquitous in all living organisms, has been used to synthesize phosphorescent GNCs for the first time. Interestingly, the synthesized phosphorescent CoA@GNCs could be further induced to generate AIE via the PO32- and Zr4+ interactions, and the observed AIE was found to be highly specific to Zr4+ ions. In addition, the enhanced phosphorescent emission could be quickly turned down by dipicolinic acid (DPA), a universal and specific component and also a biomarker of bacterial spores. Therefore, a Zr4+-CoA@GNCs-based DPA biosensor for quick, facile, and highly sensitive detection of possible spore contamination has been developed, showing a linear concentration range from 0.5 to 20 μM with a limit of detection of 10 nM. This study has demonstrated a promising future for various organic molecules containing phosphoryl moiety for the preparation of AIE-active metal nanoclusters.

An improved DNA extraction method for detecting Bacillus subtilis spores in spiked foods and beverages

Bacillus and Paenibacillus spp. are essential aerobic spoilage bacteria in various food industry sectors. Spoilage from microorganisms occurs at many points throughout food production systems. Due to their complex wall structures, spores can resist heat, radiation, chemical agents, and enzymatic treatments. An alkaline lysis and mechanical disruption combination method was developed and evaluated to counter this. This combination method effectively improved DNA extraction from B. subtilis spore cells spiked into food (solid) and beverages (liquid milk and coffee) at concentrations down to 10² CFU/mL or g when spiked into food matrices and drinks. Released DNA recoveries were 27 % and 25 % for potato salad and 38 % and 36 % for whole corn spiked at 10⁶ and 10³ CFU/mL concentrations. Conversely, there was a low recovery for wheat flour (10 % and 8.8 %) and milk powders (12 % and 25 %) at 10⁶ and 10³ CFU/mL spiked concentrations. The combination method provides rapid, specific, reliable, and accurate signature sequences identification for the detection and presence confirmation of psychrophilic and psychrotolerant spoilage spore cells, improving food spoilage assessments and food control applications.

Immediate and sensitive detection of sporulated Bacillus subtilis by microwave release and tandem mass spectrometry of dipicolinic acid

Spore lysis of Bacillus species is achieved by brief (1 min) microwave irradiation while tandem mass spectrometry (MS/MS) allows identification of the characteristic spore marker, dipicolinic acid. This rapid measurement, made on 10⁵-10⁸ spores, has significant implications for biothreat recognition.

Novel Synthesis of Thiolated Gold Nanoclusters Induced by Lanthanides for Ultrasensitive and Luminescent Detection of the Potential Anthrax Spores' Biomarker

In this study, we reported a facile, one-pot, and "green" synthesis of glutathione-protected gold nanoclusters (GSH@AuNCs) initiated by samarium (Sm³⁺) lanthanides for the first time. Sm³⁺ lanthanides more efficiently induced the formation of GSH@AuNCs with significantly enhanced luminescence than other lanthanides or heavy metal ions (Cd²⁺, Pb²⁺) did. Using this strategy, a detection for Sm³⁺ was made with a linearity range of (10.0-100.0 μM) and a limit of detection (LOD) of 0.5 μM. The Sm³⁺-based GSH@AuNCs were characterized by eco-friendliness, photostability, and low-cost synthesis with low biological toxicity and had great potential in the application for biosensing and bioimaging. They were successfully employed in the detection of dipicolinic acid (DPA), a well-reported biomarker for sensing potential infection by strongly hazardous anthrax spores. A good linear response was obtained for DPA detection ranging from 1.0 to 120.0 μM with a low LOD of 0.1 μM, which was much lower (600 times) than the infectious dosage of anthrax spores (6 × 10^-5 M). The detection was due to the strong binding affinity and strong chelation capability of DPA to Sm³⁺ lanthanides, which caused the dissociation of the aggregates with an obvious decrease or even a turning-off effect of their luminescence.

Evaluation of a Highly Efficient DNA Extraction Method for Bacillus anthracis Endospores

A variety of methods have been established in order to optimize the accessibility of DNA originating from Bacillusanthracis cells and endospores to facilitate highly sensitive molecular diagnostics. However, most endospore lysis techniques have not been evaluated in respect to their quantitative proficiencies. Here, we started by systematically assessing the efficiencies of 20 DNA extraction kits for vegetative B.anthracis cells. Of these, the Epicentre MasterPure kit gave the best DNA yields and quality suitable for further genomic analysis. Yet, none of the kits tested were able to extract reasonable quantities of DNA from cores of the endospores. Thus, we developed a mechanical endospore lysis protocol, facilitating the extraction of high-quality DNA. Transmission electron microscopy or the labelling of spores with the indicator dye propidium monoazide was utilized to assess lysis efficiency. Finally, the yield and quality of genomic spore DNA were quantified by PCR and they were found to be dependent on lysis matrix composition, instrumental parameters, and the method used for subsequent DNA purification. Our final standardized lysis and DNA extraction protocol allows for the quantitative detection of low levels (<50 CFU/mL) of B. anthracis endospores and it is suitable for direct quantification, even under resource-limited field conditions, where culturing is not an option.

Identification of pBC218/pBC210 Genes of Bacillus cereus G9241 in Five Florida Soils Using qPCR

The distribution of the virulent plasmid pBC210 of B. cereus that carries several B. anthracis genes and has been implicated in lethal anthrax-like pulmonary disease is unknown. We screened our collection of 103 B. cereus isolates and 256 soil samples using a quantitative PCR (qPCR) assay that targeted three open reading frames putatively unique to pBC210. When tested with DNA from 2 B. cereus strains carrying pBC210, and 64 Gram-positive and 55 Gram-negative bacterial species, the assay had 100% sensitivity and specificity. None of the DNA from the B. cereus isolates yielded positive amplicons but DNA extracted from five soils collected in Florida gave positive results for all three target sequences of pBC210. While screening confirms that pBC210 is uncommon in B. cereus, this study is the first to report that pBC210 is present in Florida soils. This study improves our knowledge of the distribution of pBC210 in soils and, of public health importance, the potential threat of B. cereus isolates carrying the toxin-carrying plasmid. We demonstrated that sequences of pBC210 can be found in a larger geographical area than previously thought and that finding more B. cereus carrying the virulent plasmid is a possibility in the future.

Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments

Gram-positive spore-forming sulfate reducers and particularly members of the genus Desulfotomaculum are commonly found in the subsurface biosphere by culture based and molecular approaches. Due to their metabolic versatility and their ability to persist as endospores. Desulfotomaculum spp. are well-adapted for colonizing environments through a slow sedimentation process. Because of their ability to grow autotrophically (H2/CO2) and produce sulfide or acetate, these microorganisms may play key roles in deep lithoautotrophic microbial communities. Available data about Desulfotomaculum spp. and related species from studies carried out from deep freshwater lakes, marine sediments, oligotrophic and organic rich deep geological settings are discussed in this review.

In silico and in vitro evaluation of PCR-based assays for the detection of Bacillus anthracis chromosomal signature sequences

Bacillus anthracis, the causative agent of anthrax, is a zoonotic pathogen that is relatively common throughout the world and may cause life threatening diseases in animals and humans. There are many PCR-based assays in use for the detection of B. anthracis. While most of the developed assays rely on unique markers present on virulence plasmids pXO1 and pXO2, relatively few assays incorporate chromosomal DNA markers due to the close relatedness of B. anthracis to the B. cereus group strains. For the detection of chromosomal DNA, different genes have been used, such as BA813, rpoB, gyrA, plcR, S-layer, and prophage-lambda. Following a review of the literature, an in silico analysis of all signature sequences reported for identification of B. anthracis was conducted. Published primer and probe sequences were compared for specificity against 134 available Bacillus spp. genomes. Although many of the chromosomal targets evaluated are claimed to be specific to B. anthracis, cross-reactions with closely related B. cereus and B. thuringiensis strains were often observed. Of the 35 investigated PCR assays, only 4 were 100% specific for the B. anthracis chromosome. An interlaboratory ring trial among five European laboratories was then performed to evaluate six assays, including the WHO recommended procedures, using a collection of 90 Bacillus strains. Three assays performed adequately, yielding no false positive or negative results. All three assays target chromosomal markers located within the lambdaBa03 prophage region (PL3, BA5345, and BA5357). Detection limit was further assessed for one of these highly specific assays.

Fast spore breaking by superheating

Here we present the results of Bacillus subtilis spores breaking using superheating. The spore sample was pumped through the open-ended capillary tube mounted across the heated zone. We investigated the influence of temperature in the range 120-180 °C. The heat exposure was controlled by the length of the heated zone, the inner diameter of the capillary and the sample flow rate. We found that spore treatment above 120 °C resulted in the release of DNA within 20 s.

Rapid filtration separation-based sample preparation method for Bacillus spores in powdery and environmental matrices

Authorities frequently need to analyze suspicious powders and other samples for biothreat agents in order to assess environmental safety. Numerous nucleic acid detection technologies have been developed to detect and identify biowarfare agents in a timely fashion. The extraction of microbial nucleic acids from a wide variety of powdery and environmental samples to obtain a quality level adequate for these technologies still remains a technical challenge. We aimed to develop a rapid and versatile method of separating bacteria from these samples and then extracting their microbial DNA. Bacillus atrophaeus subsp. globigii was used as a simulant of Bacillus anthracis. We studied the effects of a broad variety of powdery and environmental samples on PCR detection and the steps required to alleviate their interference. With a benchmark DNA extraction procedure, 17 of the 23 samples investigated interfered with bacterial lysis and/or PCR-based detection. Therefore, we developed the dual-filter method for applied recovery of microbial particles from environmental and powdery samples (DARE). The DARE procedure allows the separation of bacteria from contaminating matrices that interfere with PCR detection. This procedure required only 2 min, while the DNA extraction process lasted 7 min, for a total of <10 min. This sample preparation procedure allowed the recovery of cleaned bacterial spores and relieved detection interference caused by a wide variety of samples. Our procedure was easily completed in a laboratory facility and is amenable to field application and automation.

Comparative evaluation of automated and manual commercial DNA extraction methods for detection of Francisella tularensis DNA from suspensions and spiked swabs by real-time polymerase chain reaction

This study evaluated commercial automated and manual DNA extraction methods for the isolation of Francisella tularensis DNA suitable for real-time polymerase chain reaction (PCR) analysis from cell suspensions and spiked cotton, foam, and polyester swabs. Two automated methods, the MagNA Pure Compact and the QIAcube, were compared to 4 manual methods, the IT 1-2-3 DNA sample purification kit, the MasterPure Complete DNA and RNA purification kit, the QIAamp DNA blood mini kit, and the UltraClean Microbial DNA isolation kit. The methods were compared using 6 F. tularensis strains representing the 2 subspecies which cause the majority of reported cases of tularemia in humans. Cell viability testing of the DNA extracts showed that all 6 extraction methods efficiently inactivated F. tularensis at concentrations of ≤10⁶ CFU/mL. Real-time PCR analysis using a multitarget 5' nuclease assay for F. tularensis revealed that the PCR sensitivity was equivalent using DNA extracted by the 2 automated methods and the manual MasterPure and QIAamp methods. These 4 methods resulted in significantly better levels of detection from bacterial suspensions and performed equivalently for spiked swab samples than the remaining 2. This study identifies optimal DNA extraction methods for processing swab specimens for the subsequent detection of F. tularensis DNA using real-time PCR assays. Furthermore, the results provide diagnostic laboratories with the option to select from 2 automated DNA extraction methods as suitable alternatives to manual methods for the isolation of DNA from F. tularensis.

Real-time loop-mediated isothermal amplification assay for rapid and sensitive detection of anthrax spores in spiked soil and talcum powder

Loop-mediated isothermal amplification (LAMP) assay is a powerful and innovative gene amplification technique that specifically amplifies the target gene under isothermal conditions with a high degree of sensitivity, rapidity and specificity. The major advantage of the LAMP assay is monitoring of amplified products without the requirement of any sophisticated equipment. In the present study a real time LAMP assay was employed for rapid and real time detection of Bacillus anthracis spores spiked in 0.1 g of soil and talcum powder ranging from 2 to 10(7) spores. DNA was isolated from spiked soil and talcum powder using PBS containing 1% Triton X-100, and heat treatment. Isolated DNA was used as template for LAMP and PCR. LAMP amplification was obtained in 60 min under isothermal condition at 63°C by employing a set of six primers targeting the pag gene of B. anthracis. The detection limit of LAMP assay in soil and talcum powder was found to be as low as 5 spores, compared to 10(3) spores and 10(4) spores by PCR in talcum powder and soil, respectively. The findings suggest that LAMP is a more rapid and sensitive assay than PCR for detecting anthrax spores, additionally the methodology to prepare DNA from spiked samples is simple, rapid and cost effective.

A multiplex real-time PCR for identifying and differentiating B. anthracis virulent types

Bacillus anthracis is closely related to the endospore forming bacteria Bacillus cereus and Bacillus thuringiensis. For accurate detection of the life threatening pathogen B. anthracis, it is essential to distinguish between these three species. Here we present a novel multiplex real-time PCR for simultaneous specific identification of B. anthracis and discrimination of different B. anthracis virulence types. Specific B. anthracis markers were selected by whole genome comparison and different sets of primers and probes with optimal characteristic for multiplex detection of the B. anthracis chromosome, the B. anthracis pXO1 and pXO2 plasmids and an internal control (IC) were designed. The primer sets were evaluated using a panel of B. anthracis strains and exclusivity was tested using genetically closely related B. cereus strains. The robustness of final primer design was evaluated by laboratories in three different countries using five different real-time PCR thermocyclers. Testing of a panel of more than 20 anthrax strains originating from different locations around the globe, including the recent Swedish anthrax outbreak strain, showed that all strains were detected correctly.

Detection of low numbers of Bacillus anthracis spores in three soils using five commercial DNA extraction methods with and without an enrichment step

AIMS

To (i) compare the limits of detection of Bacillus anthracis spores in three soils (one Florida, one Texas, and one a commercial Garden product) by PCR using DNA extracted with five commercial extraction kits and (ii) examine if removing organic acids or adding an enrichment step utilizing a growth medium will improve the detection limits.

METHODS AND RESULTS

Bacillus anthracis spores were added to soil aliquots and used immediately with a DNA extraction kit or pretreated to remove organics or incubated overnight in a selective growth medium before the DNA extraction was performed. Using hybridization and PCR assays for capC, pag and lef genes, 10(5) -10(6) B. anthracis spores were detected in untreated Florida soil, 10(4) -10(7) spores in untreated Texas soil and 10(6) -10(7) in Garden soil. Pretreatment did not reliably improve detection. DNA from untreated and pretreated soils was suitable for hybridization but not always for PCR. When 10(1) -10(2) spores were added to the soils and allowed to amplify in a growth medium selective for B. anthracis, DNA extracted using four methods reliably produced PCR acceptable DNA positive for the B. anthracis genes.

CONCLUSIONS

The quality of DNA extracted with commercial kits appears to be influenced by the soil type and pretreatment. Yet, with an enrichment step added, four of five extraction methods produced PCR suitable DNA and detected ≤10(2) spores.

SIGNIFICANCE AND IMPACT OF THE STUDY

The enrichment step could enhance the detection of B. anthracis spores in soils and small samples contaminated with soil.

Evaluation of automated and manual commercial DNA extraction methods for recovery of Brucella DNA from suspensions and spiked swabs

This study evaluated automated and manual commercial DNA extraction methods for their ability to recover DNA from Brucella species in phosphate-buffered saline (PBS) suspension and from spiked swab specimens. Six extraction methods, representing several of the methodologies which are commercially available for DNA extraction, as well as representing various throughput capacities, were evaluated: the MagNA Pure Compact and the MagNA Pure LC instruments, the IT 1-2-3 DNA sample purification kit, the MasterPure Complete DNA and RNA purification kit, the QIAamp DNA blood mini kit, and the UltraClean microbial DNA isolation kit. These six extraction methods were performed upon three pathogenic Brucella species: B. abortus, B. melitensis, and B. suis. Viability testing of the DNA extracts indicated that all six extraction methods were efficient at inactivating virulent Brucella spp. Real-time PCR analysis using Brucella genus- and species-specific TaqMan assays revealed that use of the MasterPure kit resulted in superior levels of detection from bacterial suspensions, while the MasterPure kit and MagNA Pure Compact performed equally well for extraction of spiked swab samples. This study demonstrated that DNA extraction methodologies differ in their ability to recover Brucella DNA from PBS bacterial suspensions and from swab specimens and, thus, that the extraction method used for a given type of sample matrix can influence the sensitivity of real-time PCR assays for Brucella.

Procurement of spore-free Bacillus anthracis for molecular typing outside of BSL3 environment

AIMS

To (i) develop a protocol that would eliminate or greatly reduce sporulation within Bacillus anthracis vegetative cells, and (ii) harvest an adequate number of cells and sufficient DNA suitable for molecular methods including Riboprint analysis and pulse field gel electrophoresis (PFGE).

METHODS AND RESULTS

Seven strains of B. anthracis (Ames, French B2, Heluky, Kruger, Pasteur, Sterne, and Vollum) were grown at 37, 42 and 45 degrees C under normal air, enhanced CO(2), microaerophilic, and anaerobic conditions on solid media and subcultured in two broths with and without supplements. The bacterial cells were centrifuged and washed. Slides made from the cell pellets were stained with Malachite Green and observed for the presence of spores. Cell preparations were subjected to 80 degrees C for 30 min and processed for and analysed by either Riboprinte or PFGE. Multiple pellets of each strain were processed, stained, placed onto solid culture media, incubated for 7 days and observed for growth. The cell preparations yielded clear and reproducible results with both molecular methods. None of the cell preparations yielded growth on the culture media.

CONCLUSIONS

This method eliminated viable spores in cell preparations of B. anthracis, yet still allowed the growth of vegetative cells to provide sufficient DNA suitable for analysis by Riboprinter and PFGE.

SIGNIFICANCE AND IMPACT OF THE STUDY

This method will provide safe cell preparations, prevent instrument contamination, and may be useful for other aerobic and anaerobic spore-formers.

A Flow-Through Ultrasonic Lysis Module for the Disruption of Bacterial Spores

An automated, flow-through ultrasonic lysis module that is capable of disrupting bacterial spores to increase the DNA available for biodetection is described. The system uses a flow-through chamber that allows for direct injection of the sample without the need for a chemical or enzymatic pretreatment step to disrupt the spore coat before lysis. Lysis of Bacillus subtilis spores, a benign simulant of Bacillus anthracis, is achieved by flowing the sample through a tube whose axis is parallel to the faces of two transducers that deliver 10 W cm−2 to the surface of the tube at 1.4-MHz frequency. Increases in amplifiable DNA were assessed by real-time PCR analysis that showed at least a 25-fold increase in amplifiable DNA after ultrasonic treatment with glass beads, compared with controls with no ultrasonic power applied. The ultrasonic system and integrated fluidics are designed as a module that could be incorporated into multistep, automated sample treatment and detection systems for pathogens.

A simple method for the rapid removal of Bacillus anthracis spores from DNA preparations

This study establishes a filtration method for the safe removal of Bacillus anthracis spores which may contaminate DNA preparations. Centrifugal filtration with 0.1-microm filter units can be used following extraction of DNA from B. anthracis spores to render samples safe without compromising the sensitivity of diagnostic real-time PCR assays for B. anthracis.

Bacillus anthracis spore suspensions: determination of stability and comparison of enumeration techniques

AIM

To determine the stability and variability in concentration of spore suspensions of Bacillus anthracis (BA) spore suspensions by comparing different methods of enumeration and to detect changes, if any, under different storage conditions.

METHODS AND RESULTS

Plate and microscope counts were compared to measuring the genomic equivalents based on DNA content BA spore suspensions. We developed chemical methods to extract spore DNA and extra-spore (ES) DNA. DNA mass was determined by gel electrophoresis and QPCR assays were developed using the markers on the chromosome (rpoB) and the pXO1 plasmid (pag). The plate counts and microscope counts were very stable (for up to 900 days). The effect of freezing and the presence of additives in samples were tested for up to 300 days, and the results indicated that the additives tested and freezing did not decrease the viability or microscope counts.

CONCLUSIONS

Bacillus anthracis spore suspensions can be stored for long periods of time without significant loss of viability or clumping. The content of ES DNA was variable and changed with time.

SIGNIFICANT AND IMPACT OF THE STUDY

The study shows that BA spore suspensions can be developed for reference materials providing a uniform basis for comparing detection equipment and results from different laboratories.

Biologie moléculaire et microbiologie clinique en 2007

La biologie moléculaire est omniprésente en biologie médicale et plus particulièrement en microbiologie. De nombreux articles démontrent son importance tant dans le domaine du diagnostic que du pronostic, de l'évaluation thérapeutique, de l'épidémiologie ou des risques biologiques naturels ou non. La quantité considérable d'articles sur ce sujet n'apporte pas toujours une réponse évidente sur le rôle de la biologie moléculaire dans un laboratoire de microbiologie qu'il soit hospitalier ou non. Cette revue constitue une synthèse des apports de cette discipline en microbiologie. À partir de cet état des lieux, certaines questions se posent, par exemple : la biologie moléculaire constitue-t-elle un réel apport en microbiologie ? Dans quelles indications prescrire un examen de biologie moléculaire ? Les réponses ne sont pas toujours simples. Elles sont évidentes dans certains cas (l'hépatite C par exemple) et le sont moins dans d'autres, la tuberculose par exemple. Dans la première partie de l'article, nous avons parlé des généralités appliquées à la microbiologie. Dans cette deuxième partie, nous abordons certaines applications, reflets de l'importance prise par la biologie moléculaire en microbiologie.

Estimating amplification efficiency improves multiplex real-time PCR quantification of Bacillus licheniformis and Bacillus subtilis spores in animal feed

A multiplex real-time PCR assay was developed for absolute quantification in animal feed of Bacillus subtilis CH201 and Bacillus licheniformis CH200 spores, which constitute the viable component of the microbial growth promoter, BioPlus 2B. Spores were lysed using a bead-beating protocol. DNA was extracted and purified from the lysates with the Qiagen DNeasy Plant Kit. Two standard curves for absolute quantification were made and tested. Standard curve-1 was made from feed samples spiked with BioPlus 2B, while standard curve-2 was made from serially diluted DNA extracted from BioPlus 2B powder. Feed samples supplemented with BioPlus 2B were quantified using both standard curves. The detection limit of the assay was 10(4) CFU g(-1) of feed. The amplification efficiency (Eff) of each PCR was determined using the LinRegPCR software and Eff differences between individual samples and standards were corrected for. When compared to plate counts, standard curve-1 slightly under-estimated the number of spores (mean=-2.47% of plate counts). A spore density-dependent Eff was found, and Eff for standard curve-1 could not be determined. Standard curve-2 over-estimated spore numbers when not corrected for individual Eff (mean=+5.46% of plate counts). Standard curve-2 Eff was independent (Eff(mean)=1.96) of spore density. The assay quantified the numbers of spores in feed samples very similar to plate counts (mean=+0.47% of plate counts), when standard curve-2 was used and individual Eff was accounted for.

Bacillus anthracis virulent plasmid pX02 genes found in large plasmids of two other Bacillus species

In order to cause the disease anthrax, Bacillus anthracis requires two plasmids, pX01 and pX02, which carry toxin and capsule genes, respectively, that are used as genetic targets in the laboratory detection of the bacterium. Clinical, forensic, and environmental samples that test positive by PCR protocols established by the Centers for Disease Control and Prevention for B. anthracis are considered to be potentially B. anthracis until confirmed by culture and a secondary battery of tests. We report the presence of 10 genes (acpA, capA, capB, capC, capR, capD, IS1627, ORF 48, ORF 61, and repA) and the sequence for the capsule promoter normally found on pX02 in Bacillus circulans and a Bacillus species closely related to Bacillus luciferensis. Tests revealed these sequences to be present on a large plasmid in each isolate. The 11 sequences consistently matched to B. anthracis plasmid pX02, GenBank accession numbers AF188935.1, AE011191.1, and AE017335.3. The percent nucleotide identities for capD and the capsule promoter were 99.9% and 99.7%, respectively, and for the remaining nine genes, the nucleotide identity was 100% for both isolates. The presence of these genes, which are usually associated with the pX02 plasmid, in two soil Bacillus species unrelated to B. anthracis alerts us to the necessity of identifying additional sequences that will signal the presence of B. anthracis in clinical, forensic, and environmental samples.

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.

Requirements for the Development of Bacillus Anthracis Spore Reference Materials Used to Test Detection Systems

Bacillus anthracis spores have been used as biological weapons and the possibility of their further use requires surveillance systems that can accurately and reliably detect their presence in the environment. These systems must collect samples from a variety of matrices, process the samples, and detect the spores. The processing of the sample may include removal of inhibitors, concentration of the target, and extraction of the target in a form suitable for detection. Suitable reference materials will allow the testing of each of these steps to determine the sensitivity and specificity of the detection systems. The development of uniform and well-characterized reference materials will allow the comparison of different devices and technologies as well as assure the continued performance of detection systems. This paper discusses the special requirements of reference materials for Bacillus anthracis spores that could be used for testing detection systems. The detection of Bacillus anthracis spores is based on recognition of specific characteristics (markers) on either the spore surface or in the nucleic acids (DNA). We have reviewed the specific markers and their relevance to characterization of reference materials. We have also included the approach for the characterization of candidate reference materials that we are developing at the NIST laboratories. Additional applications of spore reference materials would include testing sporicidal treatments, techniques for sampling the environment, and remediation of spore-contaminated environments.

Real-time PCR in clinical microbiology: applications for routine laboratory testing

Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

Bacillus anthracis: toxicology, epidemiology and current rapid-detection methods

B. anthracis, the causative agent for anthrax, has been well studied for over 150 years. Due to the genetic similarities among various Bacillus species, as well as its existence in both a spore form and a vegetative state, the detection and specific identification of B. anthracis have been proven to require complex techniques and/or laborious methods. With the heightened interest in the organism as a potential biological threat agent, a large number of interesting detection technologies have recently been developed, including methods involving immunological and nucleic acid-based assay formats. The technologies range from culture-based methods to portable Total Analysis Systems based on real-time PCR. This review with 170 references provides a brief background on the toxicology and epidemiology of B. anthracis, discusses challenges associated with its detection related to genetic similarities to other species, and reviews immunological and, with greater emphasis, nucleic acid-based detection systems.

Current and developing technologies for monitoring agents of bioterrorism and biowarfare

Recent events have made public health officials acutely aware of the importance of rapidly and accurately detecting acts of bioterrorism. Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. Various commercial tests utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures are currently available to identify biological threat agents. Newer tests have also been developed to identify such agents using aptamers, biochips, evanescent wave biosensors, cantilevers, living cells, and other innovative technologies. This review describes these current and developing technologies and considers challenges to rapid, accurate detection of biothreat agents. Although there is no ideal platform, many of these technologies have proved invaluable for the detection and identification of biothreat agents.