MicrobiologyBytes

Should we destroy the remaining laboratory stocks of smallpox virus?

Now that the 20th century has passed into the domain of history books, we can retrospectively begin to assess the relative contributions that the many advances in the realm of infectious disease have actually made to public health in general. At the top of this virtuous list will surely be the discovery of antibiotics in the 1930s and the use of vaccination to eradicate smallpox as an extant human disease in the 1960s and 1970s. As clearly pointed out in a recent book by D. A. Henderson, one of the leaders of the global smallpox eradication program, this task of ridding Homo sapiens from the curse of this ancestral disease was neither easy nor without controversy. In fact, the history of the many consequences of smallpox on humankind reads like a long litany of human misery and calamitous events, but is juxtaposed with the more noble accomplishments that began with the discovery of vaccination by Jenner in 1798 and culminated with the World Health Organization (WHO) certifying the world free of smallpox in 1980. With this singular accomplishment, as many as 60–100 million individuals who would have been predicted to die of smallpox have been spared from a truly gruesome death. Nevertheless, the narrative of smallpox did not stop with its eradication as a pandemic human disease. Instead, we find ourselves still wrestling with an issue that intermingles public health policy, philosophy, national security, and bioterrorism, and affects our perceptions of research ethics with extreme pathogens in general. It boils down to a not-so-simple question: What exactly should the Victor do with the Vanquished?

Killing a Killer: What Next for Smallpox? 2010 PLoS Pathog 6(1): e1000727. doi:10.1371/journal.ppat.1000727

Related:

• W.H.O. ducks smallpox decision (again)

Melioidosis, which can present as an acute septic illness or as a chronic low-grade infection, was first described in Burma more than 100 years ago. Largely due to its recognition as a biological threat agent, current knowledge on melioidosis, caused by the Gram-negative bacterium Burkholderia pseudomallei, has increased tremendously over recent years as more and more research groups are working on this disease. The global distribution boundaries of melioidosis continue to expand well beyond the traditionally recognized endemic region of southeast-Asia and northern-Australia. For instance, new cases have been described in Brazil and southeast-Africa, although it has to be clarified whether melioidosis is indeed endemic in these regions. Of interest, phylogenetic studies have recently hypothesized that B. pseudomallei has originated in tropical Australia with subsequent spread to southeast-Asia (dubbed as the Gondwana hypothesis). Pneumonia with bacterial dissemination to distant sites and abscess formation is a common presentation. Current treatment recommendations on the basis of clinical trial evidence are parental ceftazidim or carbapenem for 10–14 days or longer as clinically indicated, followed by oral trimethoprim–sulfamethoxazole ± doxycycline for at least 12–20 weeks. This review summarizes present knowledge on the molecular characterization of B. pseudomallei and the immunology of melioidosis with a special emphasis on its potential therapeutic implications.

Immunity to Burkholderia pseudomallei. Curr Opin Infect Dis. 2009 22(2): 102-108
Largely due to its recognition as a biological threat agent, current knowledge on melioidosis, caused by the Gram-negative bacterium Burkholderia pseudomallei, has increased tremendously over the last years. This review summarizes current understanding on the molecular characterization of B. pseudomallei and the immunology of melioidosis. The genome of B. pseudomallei is composed of two chromosomes of which the largest part represents the B. pseudomallei core genome, whereas the remaining accessory genome has been associated with bacterial virulence. Virulence factors, most notably quorum sensing, type III secretion system, lipopolysaccharide and other surface polysaccharides, flagella and various factors essential for the intracellular life cycle of B. pseudomallei, have been further characterized. The neutrophils play a critical in host defense, which is initiated by the Toll-like receptors. The proinflammatory immune response – including the activation of coagulation – and its regulation have been further dissected. Severe melioidosis can probably be seen as the clinical manifestation of a pathogen recognition receptor mediated dysregulation of the immune response to invading B. pseudomallei. B. pseudomallei employs numerous tactics to evade the immune response. Studies on host-pathogen interactions in melioidosis have identified a whole range of potential new treatment targets.

Related:

• Glanders and Melioidosis – coming soon to a crowded shopping centre near you?
• Pathogenic soil bacterium is influenced by land management

Releasing highly pathogenic organisms into an urban population is a act of bioterrorism that could result in a large number of casualties. The first indication that a covert open-air release has occurred is quite likely to be individuals reporting for medical attention. If such an attack is suspected, then public health authorities would attempt to identify those individuals who have been infected in order to provide rapid treatment with the aim of reducing the possibility of disease and potential death. Aiming treatment at too small an area might miss individuals infected further down and/or up wind, whereas issues surrounding both treatment resources and serious side effects may rule out mass treatment campaigns of large sections of the population.

A new paper describes a statistical method that can estimate the origin and time of an aerosolized release of anthrax following detection of the first few cases. The method predicts where the most critically affected areas will be following the release of this highly pathogenic agent, which may enable preventative treatment of individuals at risk and protection from the disease. Previously published methods can estimate the date and scale of anthrax release but not the source location or geographic extent of human exposure. The new method uses information about the first people infected, including when they started to experience symptoms of infection and where they live and work, combined with recent weather information, such as wind direction. Anthrax has the potential to cause a large number of deaths in the event of a covert, open air release. If such a release were to occur, it is critical for public health decision makers to evaluate its extent and the potential impact on the population and then to identify the people most at risk of infection as soon as possible. It is critical to treat people as soon as possible after exposure to anthrax. While forecasts based on small numbers of early cases are less reliable than those obtained later in an outbreak, treating individuals based on early estimates is still likely to save lives overall.

Estimating the Location and Spatial Extent of a Covert Anthrax Release. 2009 PLoS Comput Biol 5(1): e1000356
Rapidly identifying the features of a covert release of an agent such as anthrax could help to inform the planning of public health mitigation strategies. Previous studies have sought to estimate the time and size of a bioterror attack based on the symptomatic onset dates of early cases. We extend the scope of these methods by proposing a method for characterizing the time, strength, and also the location of an aerosolized pathogen release. A back-calculation method is developed allowing the characterization of the release based on the data on the first few observed cases of the subsequent outbreak, meteorological data, population densities, and data on population travel patterns. We evaluate this method on small simulated anthrax outbreaks (about 25–35 cases) and show that it could date and localize a release after a few cases have been observed, although misspecifications of the spore dispersion model, or the within-host dynamics model, on which the method relies can bias the estimates. Our method could also provide an estimate of the outbreak’s geographical extent and, as a consequence, could help to identify populations at risk and, therefore, requiring prophylactic treatment. Our analysis demonstrates that while estimates based on the first ten or 15 observed cases were more accurate and less sensitive to model misspecifications than those based on five cases, overall mortality is minimized by targeting prophylactic treatment early on the basis of estimates made using data on the first five cases. The method we propose could provide early estimates of the time, strength, and location of an aerosolized anthrax release and the geographical extent of the subsequent outbreak. In addition, estimates of release features could be used to parameterize more detailed models allowing the simulation of control strategies and intervention logistics.

There is a pressing need for antiviral agents that are effective against multiple classes of viruses. Broad specificity might be achieved by targeting phospholipids that are widely expressed on infected host cells or viral envelopes. We reasoned that events occurring during virus replication (for example, cell activation or preapoptotic changes) would trigger the exposure of normally intracellular anionic phospholipids on the outer surface of virus-infected cells. A chimeric antibody, bavituximab, was used to identify and target the exposed anionic phospholipids. Infection of cells with Pichinde virus (a model for Lassa fever virus, a potential bioterrorism agent) led to the exposure of anionic phospholipids. Bavituximab treatment cured overt disease in guinea pigs lethally infected with Pichinde virus. Direct clearance of infectious virus from the blood and antibody-dependent cellular cytotoxicity of virus-infected cells seemed to be the major antiviral mechanisms. Combination therapy with bavituximab and ribavirin was more effective than either drug alone. Bavituximab also bound to cells infected with multiple other viruses and rescued mice with lethal mouse cytomegalovirus infections. Targeting exposed anionic phospholipids with bavituximab seems to be safe and effective. Our study demonstrates that anionic phospholipids on infected host cells and virions may provide a new target for the generation of antiviral agents.

Targeting inside-out phosphatidylserine as a therapeutic strategy for viral diseases. 2008 Nature Medicine 14: 1357-1362

Related:

• Unknown disease in South Africa identified as arenavirus infection

In the years during and after World War II, the Microbiological Research Establishment (MRE) at Porton Down was the UK Government’s centre for germ warfare research (or defence, depending on who you believe). There were two parts to the MRE, the part “outside the wire”, which contained among other things, the Common Cold Unit, and the section “inside the wire”, which was top secret and has been the subject of much rumour and speculation.

I recently came across an article by Bill Parker, who worked at the MRE for two years and which lifts some of the curtain of secrecy. Makes interesting reading.

Radionuclides in the environment are one of the major concerns to human health and ecotoxicology. The explosion at the Chernobyl nuclear power plant renewed interest in the role played by fungi in mediating radionuclide movement in ecosystems. As a result of these studies, our knowledge of the importance of fungi, especially in their mycorrhizal habit, in long-term accumulation of radionuclides, transfer up the food chain and regulation of accumulation by their host plants was increased. Micro-fungi have been found to be highly resilient to exposure to ionizing radiation, with fungi having been isolated from within and around the Chernobyl plant. Radioresistance of some fungal species has been linked to the presence of melanin, which has been shown to have emerging properties of acting as an energy transporter for metabolism and has been implicated in enhancing hyphal growth and directed growth of sensitized hyphae towards sources of radiation. Using this recently acquired knowledge, we may be in a better position to suggest the use of fungi in bioremediation of radioactively contaminated sites and cleanup of industrial effluent.

Fungi appear to be very resistant to radionuclides in the environment. Part of this resistance may be the smaller amount of DNA per nucleus than mammalian cells, but evidence from comparative studies between pigment and nonpigmented fungi suggest there may be other factors that confer radioresistance. Melanin pigment may provide some protection against ionizing radiation and be integral to the absorption and retention of radionuclides. Owing to the long-lived and extensive hyphal network and biomass in upper soil horizons of forest ecosystems, fungi are very efficient in absorbing radionuclides, and are an important component of long term accumulation of radionuclides. This may be why radionuclide adsorption/desorption models do not conform to observed patterns, as mycorrhizal fungi mediate soil-to-plant transfer rates. Internal translocation of radionuclides to and hyper-accumulation into harvestable fruit bodies of macro-fungi has potential for environmental remediation but needs further evaluation.

Today’s issue of Science describes how a group of scientists led by Craig Venter have built an entire bacterial genome from scratch, i.e. starting with simple laboratory chemicals and finishing with a 582,970 base pair DNA chromosome. So is this the end of the world? Have mad scientists created a Frankenstein bug which will escape the laboratory and eat the world?

Nope.

For one thing, the molecule which has been synthesized is presently just that – an inert molecule of DNA. Not until it is inserted into a “hollow” bacterial host from which the DNA has been removed can it come “alive” and start to replicate itself and direct the activities of the cell.

But more importantly, this synthetic biology project is based on an existing organism (Mycoplasma genitalium), which has been around for a long time, so it’s not exactly new. Venter’s team has reproduced this reather than creating anything new.

Finally, some bacteria degrade explosives, others prefer boiling methanol – in other words, if it is possible, nature has already thought of it. So the article published today is nothing to lose sleep over. Of course, that doesn’t mean that at some point in the future those nasty terrorists won’t build a synthetic organism which is genuinely dangerous. But they’re not going to do it working in their garage – this is a government or large corporation-scale project which is the biological equivalent of putting a person on the moon. So if you want something to worry about, worry about climate change, your grades, or the stock market.

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. 2008 Science Published Online January 24, 2008
We have synthesized a 582,970 bp Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted “watermarks” at intergenic sites known to tolerate transposon insertions. Overlapping “cassettes” of 5 to 7 kb, assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb (“1/8 genome”), and 144 kb (“1/4 genome”), which were all cloned as bacterial artificial chromosomes (BACs) in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination (TAR) cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.

Related:

• Mycoplasma laboratorium, the first synthetic organism
• Ocean Viromes
• Cytoskeletal structure of Mycoplasma mobile

The Past:
Plague has given rise to at least three major pandemics. The first (the Justinian plague) spread around the Mediterranean Sea in the 6th century AD, the second (the Black Death) started in Europe in the 14th century and recurred intermittently for more than 300 years, and the third started in China during the middle of the 19th century and spread throughout the world. Purportedly, each pandemic was caused by a different biovar of Yersinia pestis, respectively, Antiqua (still found in Africa and Central Asia), Medievalis (currently limited to Central Asia), and Orientalis (almost worldwide in its distribution).

The Present:
Given this history, plague is often classified as a problem of the past. However, it remains a current threat in many parts of the world, particularly in Africa, where both the number of cases and the number of countries reporting plague have increased during recent decades. Following the reappearance of plague during the 1990s in several countries, plague has been categorised as a re-emerging disease.

The Future:
Plague cannot be eradicated, since it is widespread in wildlife rodent reservoirs. Hence, there is a critical need to understand how human risks are affected by the dynamics of these wildlife reservoirs. For example, the likelihood of a plague outbreak in North American and Central Asian rodents, and the resulting risk to humans, is known to be affected by climate. Recent analysis of data from Kazakhstan shows that warmer springs and wetter summers increase the prevalence of plague in its main host, the great gerbil. Such environmental conditions also seem to have prevailed during the emergence of the Second and Third Pandemics – conditions that might become more common in the future.
Plague may not match the so-called “big three” diseases (malaria, HIV/AIDS, tuberculosis; see for example) in numbers of current cases, but it far exceeds them in pathogenicity and rapid spread under the right conditions. It is easy to forget plague in the 21st century, seeing it as a historical curiosity. But in our opinion, plague should not be relegated to the sidelines. It remains a poorly understood threat that we cannot afford to ignore.

Plague: Past, Present, and Future. 2008 PLoS Med 5(1): e3

Related:

• Ancient Plague
• Plague: From the 14th to the 21st century and still going strong
• A bacteriophage contributes to the pathogenicity of the plague bacillus
• How plague bacterium Yersinia pestis damages eukaryotic cells

2007 has been a record breaking year for MicrobiologyBytes, so here’s a look back at some of the highlights:

We started January off with noroviruses and ancient plague, then relaxed a bit by playing with Lego and brewing beer.

In February, we looked at yaws and Mimivirus, then went green by reducing our carbon footprint with microdiesel.

And in March we marked World Tuberculosis Day by looking at new drugs for an old foe.

April started off with an exploration of whether viruses evolve to protect their hosts, then we took out first look at colony collapse disorder affecting bees.

May was dominated by news about extreme drug resistant tuberculosis (XDR-TB) and chikungunya, then later looked at probiotics.

In June we looked at the origins of yellow fever and quorum sensing in Serratia (quorum sensing remains one of the most popular topics on MicrobiologyBytes).

July began with flesh eating bacteria and finished up with prions and Alzheimers disease.

In August, most people took a holiday and this was the quietest month of the year in terms of visitors, but we still managed to fit in Hendra, chikungunya and Marburg viruses.

September brought lots of bad news for UK farmers, so we looked at the biology of the bluetongue and foot and mouth disease virus outbreaks in the UK.

In October we covered the bacterial SOS system and debated the strategy for HPV vaccination in the UK.

November started with the terrorist threat posed by glanders and melioidosis then considered the dangers of Chlamydia infection and the opportunities presented by DNA microarrays.

We finished up the year with bacteriocins and bacterial morphology.

Phew. Overall, the most popular posts of the year were:

1. Hepatitis C Virus: a mountain to climb
2. Fungal Infections and All About Fungi
3. Infectobesity
4. Toll-Like Receptors
5. DNA microarrays

See you next year!