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Via +Terrence Lee Reed
The very microbes that helped us evolve now make us sick
"Between the mid-1990s and the mid-2000s alone, the likelihood of having a classmate with a food allergy increased by 20 per cent in the United States. In fact, over the past five decades, the incidence of all allergies and autoimmune diseases – caused by your body attacking itself – has skyrocketed."

"One thing that has changed in public health is our awareness of germs and how they spread. In response to that insight, over the past half-century our implementation of hygiene practices has spared us from debilitating infections and enormous human misery. But the new vigilance might have altered the development of our immune system, the collection of organs that fight infections and internal threats to our health."

"The idea that too clean an environment might be harmful has been dubbed ‘the hygiene hypothesis’. The concept has been perverted by some to suggest that the less clean the environment, the better."

" But its meaning is different: it is not dirt that we are missing but exposure to certain microbes that normally contribute to the development of our immune system. ‘It’s not that we aren’t exposed enough to microbes but that we’re not exposed to the right types of microbes."

"Besides the change in our exposure to microbes, our modern lives include diets much higher in sugar, salt and carbs. Now a team from Harvard and Yale has discovered that even moderate increases in salt consumption trigger activation of immune actors, known as Th17 cells, especially prevalent in such autoimmune diseases as arthritis and multiple sclerosis, to name just two."

"We are forced to conclude that the explosion of allergies and autoimmune diseases results from a mismatch between genes selected by pressures of our evolutionary past and the reality of modern life. While we have adapted in the past, we might not be able to adapt again by relying on biology alone."

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Via +Gnotic Pasta
A Nevada woman dies of a superbug resistant to every available antibiotic in the US

"Other scientists are saying this case is yet another sign that researchers and governments need to take antibiotic resistance seriously."

Although there are some steps in that direction coming from Brussels, it was not in the form of a binding law, but as a recommendation. My take is that the first phase of the process of pan-resistance has concluded, which means that nothing, even the strictest laws imposed all over the planet (which is not going to happen anytime soon), would stop the advance of resistance, and therefore of successive waves of pandemics. In many parts of the world the abuse of antibiotics is such that many different species of bacteria have acquired any of the resistance to antibiotic. The logical development of the situation, aggravated by the abuse from the food industry, and austerity measures strangling the research and the control of social health, is the appearance of super bugs already resistant to antibiotics of last resort.
Typhus and TB, even cholera are coming back, but with a vengeance, maybe Yersinia Pestis too, it takes an outbreak of antibiotics resistant TB in an area and a mere case of plague, for it to acquire resistance to antibiotics. I think there have been already cases of plague with resistance to most antibiotics in Madagascar.
In the meantime, viruses also are quietly evolving too.
It doesn't help that population growth and impoverishment of the middle classes everywhere, compounded with climate change, pollution, and war, are creating a breeding ground for epidemics, as the immune systems of the people are more vulnerable.

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Via +Andres Soolo
How a Pandemic Might Play Out Under Trump
It’s not clear that the next administration is ready to deal with an outbreak of Ebola, pandemic flu, or other emerging diseases.

“Ad-libbing, rambling, or flying off the handle can be very dangerous in an epidemic.”

"Bioethicist Art Caplan from the New York University School of Medicine envisages a quick slide towards isolation and authoritarianism. In a blog post that can only be described as pandemic fan-fiction, he imagines that a lethal mutant strain of H7N9 flu emerges in China and spreads to America. A hypothetical President Trump responds with a quick succession of moves: He seals the borders with Canada and Mexico; he quarantines sick Americans; he declares martial law, builds detention-style camps for quarantine-defiers, and uses epidemic conspiracies to launch a trade war with China."

"Trump has had a strained relationship with facts, having repeatedly and reflexively lied about matters both large and small. He has reportedly failed to seek advice from the State Department before calling foreign leaders. He is avoiding most of his daily intelligence briefings, despite his lack of prior military or political experience—“I’m, like, a smart person," he recently said. Meanwhile, Lieutenant General Mike Flynn, who will be Trump's chief counsel on national security, has shown a willingness to believe and push conspiracy theories."
"These actions portray an incoming administration with a casual disregard for evidence, an unwillingness to tap into the expertise around them, and a reckless self-confidence. They suggest that, in an outbreak, Trump is more likely to heed his own counsel than that of the Centers of Disease Control (CDC) and other relevant experts. And he is likely to project that counsel to over 17 million followers."

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Undead: The Rabies Virus Remains a Medical Mystery
"Rabies has never killed humans in great numbers, but it inspires fear far out of proportion to the risks. In part, this is because of the savage, almost supernatural mania that can grip its victims before they die. “Who is there among us,” declared a letter to The Times of London in 1830, in the midst of one citywide bout with rabid dogs, “that can leave his home in the morning, and say that he may not return in a few hours, brought back in a state that would reduce him to the desperation and frenzy of a demon, and from which a horrible death can alone relieve him?” Tales of hydrophobia filled the newspapers of 19th-century London and Paris, even though their residents were far more likely to perish from cholera or even murder; citizens organized “canicides” or “great dog massacres” to thin out the feral curs believed to carry the disease."

"That peculiar terror was one reason the great Louis Pasteur, whose two initial vaccines addressed veterinary diseases (chicken cholera and bovine anthrax), chose rabies as his first human disease to confront. His collaborator Émile Roux later wrote that rabies was selected not merely because of its medical reputation as “the most subtle and the most mysterious” of all diseases but also because, in the mind of the general public, it was “the most frightening and dreaded malady.” And indeed, in 1885, when Pasteur’s vaccine was complete, he instantly became a worldwide celebrity, winning the front-page accolades outside France that his earlier and equally impressive work (including the pasteurization process that still bears his name) never did. Pasteur’s rabies vaccine—which, because of the long latency period between bite and brain infection, could be administered days after someone was bitten—transformed an arbitrary killer into a preventable disease."

"For this reason the rabies vaccine, while an undeniable boon to human health, has nevertheless proved to be a mixed blessing for medical science. As refinement of the vaccine has brought death from rabies down to near nonexistent levels in the developed world, understanding the virus ceased to be much of a priority from either a research or public-health perspective—especially since the incurability of rabies was considered to have been established long ago. Far better to focus on vaccination, both in human bite victims and in dogs. And indeed, it has been far better, bringing us to the point today where the only nations with a serious human rabies problem are those whose scarce health resources are consumed with fighting far more prolific killers like malaria and tuberculosis. But all this success has left us with a poor understanding of how rabies actually works."

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Via +Matt Hall
Smallpox, once thought an ancient disease, may have emerged in more recent times
"Researchers compared and contrasted the 17th Century strain to those from a modern databank of samples dating from 1940 up to its eradication in 1977. Strikingly, the work shows that the evolution of smallpox virus occurred far more recently than previously thought, with all the available strains of the virus having an ancestor no older than 1580."
“This raises important questions about how a pathogen diversifies in the face of vaccination. While smallpox was eradicated in human populations, we can’t become lazy or apathetic about its evolution – and possible reemergence–until we fully understand its origins,” says Ana Duggan, a post doctoral fellow in the McMaster Ancient DNA Centre.

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Copper is good at sterilizing.
The bacteria-fighting super element that’s making a comeback in hospitals: copper
"Ancient Egyptians used copper to sterilize chest wounds and drinking water. Greeks, Romans and Aztecs relied on copper compounds to treat burns, headaches and ear infections. Thousands of years later, the ancient therapeutic is being embraced by some hospitals because of its ability to kill bacteria and other microbes on contact, which can help reduce deadly infections."

"At least 15 hospitals across the country have installed, or are considering installing, copper components on “high-touch” surfaces easily contaminated with microbes — faucet handles on sinks, cabinet pulls, toilet levers, call buttons and IV poles."

"On any given day, about 1 in 25 patients in acute-care hospitals has at least one health-care-associated infection, according to the Centers for Disease Control and Prevention. Pneumonia and surgical-site infections are among the most common. In 2011, about 75,000 patients with health-care-associated infections died in the hospital."

"Hospital officials aren’t the only ones interested in copper. Hartsfield-Jackson Atlanta International Airport installed drinking fountains retrofitted with antimicrobial copper surfaces."

Another link:
Copper’s role in tackling superbugs

"Researchers have found that MRSA bacteria remain fully active for days on stainless steel surfaces, whereas on brass (an alloy of copper and zinc), they die in less than five hours on a moist surface and on pure copper they are eliminated in under 30 minutes. On a dry surface this happens in just a few minutes."

How copper kills
"The Southampton research team has shown that copper works in several different ways to shut down bacterial cells’ chemistry and physiology. Using ‘quenching agents’ to inhibit the action of copper, the team worked out that the metal releases positively charged ions and reactive oxygen species, which quickly kill any bacterial cells that touch it."
“We have seen that copper completely destroys the bacteria’s DNA in minutes so they can’t go on to become resistant,” says Bill.
"Copper destroys not only chromosomal DNA, but also plasmids, which are circular pieces of DNA that confer antibiotic resistance. These plasmids can move between bacteria, passing on the antibiotic resistance to different bacterial species. Copper therefore not only kills these agents, but also prevents mutation and resistance transfer to other potential superbugs."

"There have been further exciting developments, with the discovery that copper can help to prevent the spread of respiratory viruses, which are linked to severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). One such virus – human coronavirus 229E – can survive on surface materials including ceramic tiles, glass, rubber and stainless steel for at least five days. However, research at Southampton has shown that with exposure to copper, the virus is inactivated within a few minutes, before being completely and irreversibly destroyed."

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Multidrug-resistant TB rates soaring in west Africa, WHO warns
Researchers find 35% of people who had already been treated for tuberculosis were infected with drug-resistant strain

The worrying thing is that you don't need infected people travelling for the bacteria to transfer resistance between them. Slowly but relentlessly they communicate their antibiotic resistant genes, spreading their influence.

Horizontal Gene Transfer
"Horizontal gene transfer, or the process of swapping genetic material between neighboring “contemporary” bacteria, is another means by which resistance can be acquired. Many of the antibiotic resistance genes are carried on plasmids, transposons or integrons that can act as vectors that transfer these genes to other members of the same bacterial species, as well as to bacteria in another genus or species. Horizontal gene transfer may occur via three main mechanisms: transformation, transduction or conjugation."

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The Black Death is lurking in the dark.
When death came calling: how the plague swept through Hong Kong (1894)

"The word "plague" might be redolent of biblical retribution and medieval misery, but the disease itself has not been consigned to history. In fact, since the early 1990s, plague has been making a comeback. Over the past 20 years, more than 50,000 human cases have been reported and the World Health Organisation has classified it as a re-emerging disease."
"Plague first arose in China," says Dr Elisabeth Carniel, head of the Yersinia Research Unit at the Institut Pasteur, the leading French research institute, and director of the WHO's Collaborating Centre of Reference and Research on Yersinia. "A number of teams have conducted genetic studies to pinpoint the origin of the plague bacillus and what we found is amazing. Most bacteria are millions of years old and arose long before human beings. Yersinia pestis, however, is only 3,000 years old. It's the youngest pathogen we know - in terms of evolution it's like a newborn baby."

"Plague manifests in three forms, depending on the route of infection. The most common form is bubonic plague. When a plague-carrying flea bites a person, the bacteria wash into the wound and travel to lymph nodes in the armpit, groin and neck. The lymph nodes enlarge, forming the "buboes" that give this form of plague its name."
"Without treatment the victim experiences seizures, cramps, a hacking cough, acute fever and delirium. The skin blackens as gangrene sets in at the fingers, toes, lips and nose, causing excruciating pain. Death occurs in 40 to 80 per cent of victims within about seven days."

"If the bacteria reach the lungs, the second form - pneumonic plague - develops. Pneumonic plague can be transmitted directly from person to person via coughs and sneezes, so it can spread extremely fast. The mortality rate is 100 per cent and death comes quickly, in one to three days."

"The third and rarest form is septicemic plague, which occurs if the bacillus enters the bloodstream. It is so deadly that the victim can die even before symptoms appear."

"From its birthplace in China, the plague bacillus went on the rampage and caused major pandemics on three occasions. The first pandemic, the Justinian plague, swept around the Mediterranean in the sixth century. It killed an estimated 50 per cent of Europe's population before dying out in the seventh century."

"The second pandemic started in the mid-14th century and followed the Silk Road, arriving in Europe in 1348, where it became known as the Black Death.

"The third pandemic was the one that brought Hong Kong to its knees. It started in Yunnan province in the 1850s and, over several decades, made gradual progress along trade routes until it reached Canton (now Guangzhou) in 1894. With daily water traffic between Canton and Hong Kong, it was inevitable that plague would spread to the colony. The first cases were identified in Tai Ping Shan at the beginning of May."

"After the British arrived, in the 1840s, they established Tai Ping Shan as a settlement for Chinese workers. As the population grew, the district's tenement houses were sub-divided into tiny, window-less dwellings and large multi-generational families were shoe-horned into them. There was no fresh water supply, no sewerage system and no proper drainage. Contemporary reports describe a hellhole - the inhabitants lived in abject squalor, the streets were mired in filth and the stench was overpowering. It was the kind of place where pathogens thrived and diseases spread like wildfire."

"This was the age of steamships and railways - rapid forms of transport that allowed the plague to diffuse globally at a faster speed than ever before."

"Plague is not just a disease of the poor. There are human cases in the US every year, usually when domestic cats come into contact with infected rodents and then return home, infecting their owners."

"Plague scientists are also concerned about global warming, which might allow the plague bacillus to expand its geographical range."

"It's the most pathogenic agent on Earth but we still don't know what makes it so virulent. It seems to become invisible to the host's immune system, but we don't know how. And in some parts of the world we don't know which animals are carrying the plague. This information is critical in trying to control the spread."

"Plague was the first biological agent to be used as a weapon. In 1346, the Mongol army suffered an outbreak of plague while besieging the Genoese-controlled trading city of Caffa, in modern-day Crimea. Turning a crisis into an opportunity, the soldiers hurled plague-ridden corpses over the city walls. The terrified Italian merchants fled back to Europe by ship, carrying the plague with them."

"It's becoming increasingly difficult to obtain the different strains of Yersinia pestis, to collaborate with scientists from other countries and to publish academic papers. No one wants to risk plague falling into the wrong hands but the danger is that we might have to stop working on it. And if we do that, and a terrorist releases the bacillus, there will be less scientific knowledge as to how to prevent and control the spread of disease."

"It's essential that we keep working. Although the number of human cases is very small when compared to some other diseases, it would be a mistake to overlook the threat it might become. After the first and second pandemics, plague seemed to go away. Both times people assumed it had gone forever. Both times they were wrong. It may remain silent for years but it will always reappear. It's here to stay and I don't think we'll ever get rid of it."

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Animal TB threatens human health say vets and doctors
Animal tuberculosis, which is spread through contaminated food, is a greater threat to human health than previously realised, leading doctors and vets have warned.

"Studies in Mexico suggest 28% of all tuberculosis cases are down to zoonotic TB but a study in India put the figure at 9% and one in children in California suggested a figure of 45%."

"One of the biggest issues the report raises is the unknown scale of the problem."

"The best estimates suggest there are around 121,000 new cases of animal TB each year."

"Ten thousand die every year from this disease."

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A good movie about a pandemic.
Contagion (2011)
Considering my interest in epidemics is strange that I haven't watched this movie before. As I am now with a cold with fever, coughing, and with running nose, I think it's a good time to watch this movie, which is very realistic about something that might happen in real life. The science behind the movie is rather accurate and how they deal with possible pandemics, showing the unpreparedness we face in the wake of a global calamity.
This is serious stuff in a blood curdling movie, a reminder of the uncertainty and the fear that only get worse when we realize that all hell can break loose.

And here an article about the role of structural biology in viruses that is shown in the movie:
Hollywood Science: Structural Biology in 'Contagion'

"The creators of "Contagion" greatly emphasized accurately depicting a viral outbreak and the scientific response to such a pandemic."
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