A genomics-based approach to biodefence preparedness

[Quo vadis in vaccines: From the empirical approach to the new wave of technology]

The development of vaccines is a multifactorial process that has evolved and expanded, particularly over the last decades. The search for immunogenic vaccines that are also acceptably safe and tolerable enacted continuous technological advances in this field. In this regard, the technology applied to vaccines can historically be divided into 3 approaches: the empirical approach, the modern approach, and the new technological wave. The empirical approach for vaccine development includes whole micro-organisms, attenuation, inactivation, cell cultures and sub-unit vaccines. The modern approach contributed to leaps and bounds to vaccine development using chemical conjugation, as well as recombinant protein DNA technology and reverse vaccinology. Lastly, the new technological wave includes, among others, bioconjugation, viral vectors, synthetic biology, self-amplification of messenger RNA, generalized modules for membrane antigens, structural vaccinology and the new adjuvants.

Investigating the predictability of essential genes across distantly related organisms using an integrative approach

Rapid and accurate identification of new essential genes in under-studied microorganisms will significantly improve our understanding of how a cell works and the ability to re-engineer microorganisms. However, predicting essential genes across distantly related organisms remains a challenge. Here, we present a machine learning-based integrative approach that reliably transfers essential gene annotations between distantly related bacteria. We focused on four bacterial species that have well-characterized essential genes, and tested the transferability between three pairs among them. For each pair, we trained our classifier to learn traits associated with essential genes in one organism, and applied it to make predictions in the other. The predictions were then evaluated by examining the agreements with the known essential genes in the target organism. Ten-fold cross-validation in the same organism yielded AUC scores between 0.86 and 0.93. Cross-organism predictions yielded AUC scores between 0.69 and 0.89. The transferability is likely affected by growth conditions, quality of the training data set and the evolutionary distance. We are thus the first to report that gene essentiality can be reliably predicted using features trained and tested in a distantly related organism. Our approach proves more robust and portable than existing approaches, significantly extending our ability to predict essential genes beyond orthologs.

Pathogen microevolution in high resolution

Microbial genomics has revolutionized infectious diseases and epidemiology research and is facilitating the tracking and containment of emerging biological threats. Among the most serious contemporary infectious agents are multiple antibiotic-resistant strains of the human pathogen Staphylococcus aureus, which present a formidable public health challenge that is no longer limited to hospitalized patients. To address key hypotheses regarding microbial strain evolution or virulence, conventional genotyping methods do not offer enough power to resolve minor changes between closely related strains. The application of next-generation high-throughput genotyping technologies, as illustrated in a recent analysis of a highly resistant S. aureus strain, can provide new clues about the geographical origin and intrahospital spread of important microbial pathogens.

Bioterrorism

Bioterrorism is defined as the deliberate and malicious deployment of microbial agents or their toxins as weapons in a non-combat setting, represents perhaps the most overt example of human behavior impacting epidemic infectious diseases. There is historical precedent for the use of biological agents against both military and civilian populations. The use of biological (and chemical) agents as weapons of war has been well documented. The German biological warfare program during World War I included covert infections of Allied livestock with anthrax and glanders. The Japanese army began conducting experiments on the effects of bacterial agents of biowarfare on Chinese prisoners in occupied Manchuria in 1932 at their infamous Unit 731. The United States began its own offensive biological weapons program in 1942 and, during its 28-year official existence, weaponized and stockpiled lethal biological agents, such as anthrax, as well as incapacitating agents, such as the etiologic agent of Q fever. There are some recent examples of bioterrorism, though not necessarily resulting in attacks causing morbidity or mortality, may serve as harbingers of future events. Saddam Hussein's regime in Iraq developed and deployed anthrax and botulinum-laden warheads in the years leading up to the Gulf War. The reasons that these weapons were never used in an actual attack probably had more to do with the implicit threat of overwhelming US retaliation and Iraqi technological deficiencies rather than the regime's reluctance to violate any moral principles. Biological agents have also been used to forward political ideologies: in 1984 a religious cult, intent on influencing voter turnout during a local election, contaminated restaurant salad bars in The Dalles, Oregon.

Statistical methods for building random transposon mutagenesis libraries

During the construction of random transposon mutagenesis libraries, four essential statistical issues arise: (1) Computing basic probability results for number of open reading frame knockouts. (2) Estimating the number of new open reading frames that will be knockouts in the next set of clones. (3) Estimating the number of essential open reading frames. (4) Computing the probability that an open reading frame is essential given the distribution of insertions. This chapter examines these issues and evaluates potential solutions using three different approaches: Efron and Thisted's estimator, Will and Jacobs's parametric bootstrap, and Blades and Broman's Gibbs sampler. In doing so, this chapter provides guidance for using the R statistical project to solve these problems.

GeneChip resequencing of the smallpox virus genome can identify novel strains: a biodefense application

We developed a set of seven resequencing GeneChips, based on the complete genome sequences of 24 strains of smallpox virus (variola virus), for rapid characterization of this human-pathogenic virus. Each GeneChip was designed to analyze a divergent segment of approximately 30,000 bases of the smallpox virus genome. This study includes the hybridization results of 14 smallpox virus strains. Of the 14 smallpox virus strains hybridized, only 7 had sequence information included in the design of the smallpox virus resequencing GeneChips; similar information for the remaining strains was not tiled as a reference in these GeneChips. By use of variola virus-specific primers and long-range PCR, 22 overlapping amplicons were amplified to cover nearly the complete genome and hybridized with the smallpox virus resequencing GeneChip set. These GeneChips were successful in generating nucleotide sequences for all 14 of the smallpox virus strains hybridized. Analysis of the data indicated that the GeneChip resequencing by hybridization was fast and reproducible and that the smallpox virus resequencing GeneChips could differentiate the 14 smallpox virus strains characterized. This study also suggests that high-density resequencing GeneChips have potential biodefense applications and may be used as an alternate tool for rapid identification of smallpox virus in the future.

The potential of antibody-mediated immunity in the defence against biological weapons

Antibody-mediated immunity (AMI) has been used for the treatment and prevention of infectious diseases for > 100 years, and has a remarkable record of safety, efficacy and versatility. AMI can be used for defence against a wide variety of biological weapons, and passive antibody (Ab) therapy has the potential to provide immediate immunity to susceptible individuals. Recent advances in the Ab field make it possible to generate Abs with enhanced antimicrobial functions. There are significant gaps in our understanding of Ab function, such that the development of Ab-based strategies remains a largely empirical exercise. Nevertheless, the advantages inherent in the therapeutic and prophylactic use of AMI provide a powerful rationale for continued development that will undoubtedly yield many new vaccines and therapeutic Abs.

INFECTIOUS DISEASES

The emergence of new pathogens, or the concern about bioterrorism, has brought an added urgency to the development of more efficient and rapid methods to detect pathogens and predict their potential virulence. Till date, DNA testing in microbiology has been directed predominantly to the detection of organisms that are difficult to culture in vitro, or for various reasons the growth is unlikely. DNA analysis can be used successfully in infections in which there is a mix of pathogens. Apart from the straightforward diagnostic applications, DNA microbiological testing has been used to detect antimicrobial resistance or toxigenic forms of E. coli. More recently, the availability of DNA technology to quantitate HCV and HIV has been useful in planning and monitoring treatment. The pathogenesis of many infections, particularly viral ones, can also be realized from experimental strategies based on light and electron microscopy, cell culture and immunoassay. The advantages that are provided by DNA techniques include the ability to detect latent (non-replicating) viruses and to localize their genomes to nuclear or cytoplasmic regions within cells. Nucleic acid probe techniques (NAT) can also be manipulated to enable a broad spectrum of serotypes to be detectable. This is particularly valuable in those emerging infections where the underlying serotypes are unknown.

Making prevention pay

Funding for biodefense is spurring new vaccine and anti-infective programs at several biotech companies.