Current Laboratory Methods for Biological Threat Agent Identification

Plummer M. The evolution of rapid antigen detection systems and their application for COVID-19 and other serious respiratory infectious diseases

Making the correct diagnosis of a patient seeking medical attention is the ultimate goal of a practicing physician, irrespective of whether the cause of the patient's condition is infectious or non-infectious. Antigen detection tests can be used to aid in the diagnosis of various infectious-related disorders including COVID-19 where it has become especially important due to the serious nature of this disease and its worldwide prevalence. These tests closely mimic one of the earliest prototypes - the urine pregnancy test - and as a result they have gained wide acceptance based on their overall simplicity, low cost and relative accuracy. In some situations, especially as a screening test, they can be used instead of the more technically demanding and complex molecular and serologic assays that are still useful and helpful under many different circumstances. Antigen detection systems are based on finding a particular immunogenic component, typically a protein or polysaccharide molecule, that is both unique and an integral part of the pathogen or other biological entity. Because these tests generally provide only qualitative results, they often need to be supplemented with other and sometimes more sophisticated laboratory-based diagnostic procedures to corroborate the initial test result. In this review, we first describe general background information on antigen-detection methods, including any unique aspects of their overall design, and then follow with an extensive description on the merits and limitations of these tests for detecting COVID-19 and, to a lesser extent, for other serious respiratory diseases caused by three common bacterial pathogens - Streptococcus pyogenes, Streptococcus pneumoniae and Legionella pneumophila.

Evaluation of an Electrochemiluminescence Assay for the Rapid Detection of Abrin Toxin

In this article, we detail a comprehensive laboratory evaluation of an immunoassay for the rapid detection of abrin using the Meso Scale Diagnostics Sector PR2 Model 1800. For the assay evaluation, we used inclusivity and exclusivity panels comprised of extracts of 11 Abrus precatorius cultivars and 35 near-neighbor plants, 65 lectins, 26 white powders, 11 closely related toxins and proteins, and a pool of 30 BioWatch filter extracts. The results show that the Meso Scale Diagnostics abrin detection assay exhibits good sensitivity and specificity with a limit of detection of 4 ng/mL. However, the dynamic range of the assay for the quantitation of abrin was limited. We observed a hook effect at higher abrin concentrations, which can lead to potential false negative results. A modification of the assay protocol that incorporates extra wash steps can decrease the hook effect and the potential for false negative results.

Affinity capture mass spectrometry of biomarker proteins using peptide ligands from biopanning

Affinity capture mass spectrometry was used to isolate and ionize protein A from Staphylococcus aureus from both a commercial source and cell culture lysate using matrix assisted laser desorption/ionization (MALDI) mass spectrometry. Two surfaces are compared: gold surfaces with immunoglobulin G covalently immobilized and silica surfaces with a covalently bound small peptide discovered via biopanning. A detection limit of 2.22 bacterial cells/mL of culture fluid was determined for the immobilized peptide surfaces. This study emphasizes the ability to use peptide ligands to effectively capture a biomarker protein out of a complex mixture. This demonstrates the potential to use biopanning to generate capture ligands for a large variety of target proteins and subsequently detect the captured protein using MALDI mass spectrometry.

Analysis of suspicious powders following the post 9/11 anthrax scare

BACKGROUND

Following the 9/11 terrorist attacks, SET Environmental, Inc., a Chicago-based environmental and hazardous materials management company received a large number of suspicious powders for analysis.

METHODS

Samples of powders were submitted to SET for anthrax screening and/or unknown identification (UI). Anthrax screening was performed on-site using a ruggedized analytical pathogen identification device (R.A.P.I.D.) (Idaho Technologies, Salt Lake City, UT). UI was performed at SET headquarters (Wheeling, IL) utilizing a combination of wet chemistry techniques, infrared spectroscopy, and gas chromatography/mass spectroscopy. Turnaround time was approximately 2-3 hours for either anthrax or UI.

RESULT

Between October 10, 2001 and October 11, 2002, 161 samples were analyzed. Of these, 57 were for anthrax screening only, 78 were for anthrax and UI, and 26 were for UI only. Sources of suspicious powders included industries (66%), U.S. Postal Service (19%), law enforcement (9%), and municipalities (7%). There were 0/135 anthrax screens that were positive.

CONCLUSIONS

There were no positive anthrax screens performed by SET in the Chicago area following the post-9/11 anthrax scare. The only potential biological or chemical warfare agent identified (cyanide) was provided by law enforcement. Rapid anthrax screening and identification of unknown substances at the scene are useful to prevent costly interruption of services and potential referral for medical evaluation.

Early indicators of exposure to biological threat agents using host gene profiles in peripheral blood mononuclear cells

Background

Effective prophylaxis and treatment for infections caused by biological threat agents (BTA) rely upon early diagnosis and rapid initiation of therapy. Most methods for identifying pathogens in body fluids and tissues require that the pathogen proliferate to detectable and dangerous levels, thereby delaying diagnosis and treatment, especially during the prelatent stages when symptoms for most BTA are indistinguishable flu-like signs.

Methods

To detect exposures to the various pathogens more rapidly, especially during these early stages, we evaluated a suite of host responses to biological threat agents using global gene expression profiling on complementary DNA arrays.

Results

We found that certain gene expression patterns were unique to each pathogen and that other gene changes occurred in response to multiple agents, perhaps relating to the eventual course of illness. Nonhuman primates were exposed to some pathogens and the in vitro and in vivo findings were compared. We found major gene expression changes at the earliest times tested post exposure to aerosolized B. anthracis spores and 30 min post exposure to a bacterial toxin.

Conclusion

Host gene expression patterns have the potential to serve as diagnostic markers or predict the course of impending illness and may lead to new stage-appropriate therapeutic strategies to ameliorate the devastating effects of exposure to biothreat agents.

An integrated culture and real-time PCR method to assess viability of disinfectant treated Bacillus spores using robotics and the MPN quantification method

Using robotics and the MPN technique, a 96-microwell method was developed to compare two procedures for enumeration of viable chlorine-treated B. atrophaeus spores: broth-culture enrichment followed by real-time polymerase chain reaction analysis; and filter plating on agar. Recoveries of chlorine-treated spores were improved by broth enrichment over filter plating, whereas recoveries of non-treated spores were not different in the two procedures.

Fiber-optic microsphere-based arrays for multiplexed biological warfare agent detection

We report a multiplexed high-density DNA array capable of rapid, sensitive, and reliable identification of potential biological warfare agents. An optical fiber bundle containing 6000 individual 3.1-mum-diameter fibers was chemically etched to yield microwells and used as the substrate for the array. Eighteen different 50-mer single-stranded DNA probes were covalently attached to 3.1-mum microspheres. Probe sequences were designed for Bacillus anthracis, Yersinia pestis, Francisella tularensis, Brucella melitensis, Clostridium botulinum, Vaccinia virus, and one biological warfare agent (BWA) simulant, Bacillus thuringiensis kurstaki. The microspheres were distributed into the microwells to form a randomized multiplexed high-density DNA array. A detection limit of 10 fM in a 50-microL sample volume was achieved within 30 min of hybridization for B. anthracis, Y. pestis, Vaccinia virus, and B. thuringiensis kurstaki. We used both specific responses of probes upon hybridization to complementary targets as well as response patterns of the multiplexed array to identify BWAs with high accuracy. We demonstrated the application of this multiplexed high-density DNA array for parallel identification of target BWAs in spiked sewage samples after PCR amplification. The array's miniaturized feature size, fabrication flexibility, reusability, and high reproducibility may enable this array platform to be integrated into a highly sensitive, specific, and reliable portable instrument for in situ BWA detection.

The evolving field of biodefence: therapeutic developments and diagnostics

Bioweapons are a clear threat to both military and civilian populations. Here, the latest advances in the pursuit of inhibitors against biothreat threat toxins, current therapeutic strategies for treating biodefence related pathogens, and strategies for improving detection and exposure survivability are covered.

There are numerous lead therapeutics that have emerged from drug discovery efforts. However, many of these are toxic and/or fail to possess conventional drug-like properties. One clear advantage of small (non-peptidic) molecules is that they possess scaffolds that are inherently more likely to evolve into real therapeutics.

One of the major obstacles impeding the translation of these lead therapeutics into viable drugs is the lack of involvement of the pharmaceutical industry, which has been discovering leads and translating them into drugs for decades. The expertise of the pharmaceutical industry therefore needs to be more effectively engaged in developing drugs against biothreat agents.

New methods for rapidly detecting and diagnosing biothreat agents are also in development. The detection and diagnosis of biothreats is inherently linked with treatment. The means for detecting the release of bioweapons are being deployed, and new technologies are shortening the timeframe between initial sample collection and conclusive agent determination. However, the organization of this process is imperfect.

At present, a unifying entity that orchestrates the biodefence response is clearly needed to reduce the time-to-drug process and redundancies in drug development efforts. Such a central entity could formulate and implement plans to coordinate all participants, including academic institutions, government agencies and the private sector. This could accelerate the development of countermeasures against high probability biothreat agents.

The threat of bioterrorism and the potential use of biological weapons against both military and civilian populations has become a major concern for governments around the world. For example, in 2001 anthrax-tainted letters resulted in several deaths, caused widespread public panic and exerted a heavy economic toll. If such a small-scale act of bioterrorism could have such a huge impact, then the effects of a large-scale attack would be catastrophic. This review covers recent progress in developing therapeutic countermeasures against, and diagnostics for, such agents.

Implementation of Biosurety Systems in a Department of Defense Medical Research Laboratory

New biosurety regulations and guidelines were implemented in 2003 because of increased concern for the safety and security of biological select agents and toxins (BSAT) that may be used as weapons of mass destruction. Biosurety is defined as the combination of security, biosafety, agent accountability, and personnel reliability needed to prevent unauthorized access to select agents of bioterrorism. These new regulations will lead to increased scrutiny of the use of select biological agents in registered research laboratories, but the regulations may have unintended effects on cost, progress, and perceptions in programs previously considered part of the academic research community. We review the history of biosurety, evolving guidelines, implementation of the regulations, and impacts at the lead research laboratory for medical biological defense for the Department of Defense.

Detection and differentiation of biological species using microcalorimetric spectroscopy

We report on the application of infrared (IR) microcalorimetric spectroscopy ( micro -CalSpec) to the identification and detection of trace amounts of biological species. Our approach combines principles of photothermal IR spectroscopy with ultrasensitive microcantilever (MC) thermal detectors. We have obtained photothermal IR spectra for DNA and RNA bases and for Bacillus Cereus (an anthrax simulant) in the wavelength range of 2.5-14.5 micro m (4000-690 cm(-1)). The measurements are accomplished by absorbing biological materials directly on a MC thermal detector. The main advantage of the developed micro -CalSpec is its unprecedented sensitivity as compared to any of the previously explored IR techniques, including FTIR and photothermal FTIR methods. Our results demonstrate that <10(-9)g of a biological sample is sufficient to obtain its characteristic micro -CalSpec spectrum that contains information-rich chemical (vibrational) signatures. This opens up a new opportunity to create inexpensive high-throughput analytical systems for biochemical detection.

Reagentless detection of microorganisms by intrinsic fluorescence

Quick and accurate detection of microbial contamination is accomplished by a unique combination of leading-edge technologies described in this and the accompanying paper. In this contribution, a hand-held prototype instrument is described which is capable of statistically sampling the environment for microbial contamination and determining cell viability. The technology is sensitive enough to detect very low levels ( approximately 20 cells/cm(2) or cm(3)) of microbes in seconds.

Taxonomic identification of microorganisms by capture and intrinsic fluorescence detection

Quick and accurate detection of microbial contamination is accomplished by a unique combination of leading edge technologies described in this and the accompanying article. Microbe capture chips, used with a prototype fluorescence detector, are capable of statistically sampling the environment for pathogens (including spores), identifying the specific pathogens/exotoxins, and determining cell viability where appropriate.

Detection of anthrax simulants with microcalorimetric spectroscopy: Bacillus subtilis and Bacillus cereus spores

Recent advances in the development of ultrasensitive micromechnical thermal detectors have led to the advent of novel subfemtojoule microcalorimetric spectoscopy (CalSpec). On the basis of principles of photothermal IR spectroscopy combined with efficient thermomechanical transduction, CalSpec provides acquisition of vibrational spectra of microscopic samples and absorbates. We use CalSpec as a method of identifying nanogram quantities of biological micro-organisms. Our studies focus on Bacillus subtilis and Bacillus cereus spores as simulants for Bacillus anthracis spores. Using CalSpec, we measured IR spectra of B. subtilis and B. cereus spores present on surfaces in nanogram quantities (approximately 100-1,000 spores). The spectra acquired in the wavelength range of 690-4000 cm(-1) (2.5-14.5 microm) contain information-rich vibrational signatures that reflect the different ratios of biochemical makeup of the micro-organisms. The distinctive features in the spectra obtained for the two types of microorganism can be used to distinguish between the spores of the Bacillus family. As compared with conventional IR and Fourier-transform IR microscopic spectroscopy techniques, the advantages of the present technique include significantly improved sensitivity (at least a full order of magnitude), absence of expensive IR detectors, and excellent potential for miniaturization.

Development of a 5' nuclease assay to detect ciprofloxacin resistant isolates of the biowarfare agent Yersinia pestis

The detection of antibiotic resistance in agents of biowarfare is extremely critical in order to start appropriate therapy in a timely manner. We have developed a 5' nuclease assay to detect ciprofloxacin resistance (Cip(r)) in Yersinia pestis. Two groups of fluorogenic probes were developed. The first group included a probe homologous to the wild type Y. pestis gyrA sequence with two corresponding probes that were homologous with two different mis-sense mutations in codon 81 of GyrA. The second group of probes included a wild type probe and two corresponding probes that recognized mis-sense mutations in codon 83 or gyrA. These probes specifically reacted only with the homologous DNA sequences. The 5' nuclease assay was sensitive to 1 pg (approximately 1 colony forming unit) of starting template and could be used on semi-purified DNA. We tested our optimized assay against a group of 38 Cip(r) Y. pestis isolates and demonstrated that it was accurate at determining the gyrA allele encoded by these strains. The 5' nuclease assay performed on the LightCycler proved to be sensitive, rapid and accurate at identification of Cip(r) Y. pestis and thus should be useful in characterization of this organism in the event of a future act of bioterrorism.

Diagnostic analyses of biological agent-caused syndromes: laboratory and technical assistance

The impact of a bioterrorism attack can be greatly reduced by collaboration among primary healthcare providers, laboratories, the veterinary community, public health officials, and emergency response personnel. Improved communication and coordination are essential to make this happen. As a first-line provider, the emergency physician must keep in mind the possibility of bioterrorism and alert the laboratory so that samples can be processed in the correct fashion. New and exciting developments in laboratory organization, communication, and diagnostic capabilities will ensure that all patients receive the best possible care.

Development and evaluation of a fluorogenic 5' nuclease assay to detect and differentiate between Ebola virus subtypes Zaire and Sudan

The ability to rapidly recognize Ebola virus infections is critical to quickly limit further spread of the disease. A rapid, sensitive, and specific laboratory diagnostic test is needed to confirm outbreaks of Ebola virus infection and to distinguish it from other diseases that can cause similar clinical symptoms. A one-tube reverse transcription-PCR assay for the identification of Ebola virus subtype Zaire (Ebola Zaire) and Ebola virus subtype Sudan (Ebola Sudan) was developed and evaluated by using the ABI PRISM 7700 sequence detection system. This assay uses one common primer set and two differentially labeled fluorescent probes to simultaneously detect and differentiate these two subtypes of Ebola virus. The sensitivity of the primer set was comparable to that of previously designed primer sets, as determined by limit-of-detection experiments. This assay is unique in its ability to simultaneously detect and differentiate Ebola Zaire and Ebola Sudan. In addition, this assay is compatible with emerging rapid nucleic acid analysis platforms and therefore may prove to be a very useful diagnostic tool for the control and management of future outbreaks.