Sunday, January 31, 2010

More Pro and Anti- Bubonic Plague Theories- how exciting!

In tandem with what Professor Latto presented in lecture, there is some disagreement as to what really caused the Pandemic widely known as “The Black Death.” I wanted to find some compelling evidence for one side or the other, but, in reality, I just found more information on how The Pandemic could have been caused by the Bubonic Plague and then why it was not. One anti-Bubonic Plague theory suggests that a virus like Ebola caused the Plague since the disease spread from person to person so quickly. In addition, the outbreak occurred and ended very suddenly which is typical of a virus. Another theory suggests that anthrax is the real culprit. Not too long before the Plague broke out in Europe, Europeans, particularly the English, began to consume domesticated animals, mostly cows, as a source of protein instead of wild game. It’s been suggested that this situation was ideal for cattle-born anthrax to quickly infect a lot of people in Europe.

However the theory that I found most disturbing was one in the Pro-Bubonic Plague camp. Many scientists agree that the theory suggesting that infected rats spread the Bubonic Plague all over Europe is somewhat flawed because it seems unreasonable to assert that rats can travel that quickly when it’s known that rats don’t usually stray too far from where they are born during their lifetime nor can they move hundreds of miles a day, even a week. So, it’s been hypothesized that human fleas, Pulex irritans, spread the Plague from person to person and from city to city. I find this reasonable for two reasons: humans at this time in history where very, very dirty and, as demonstrated by Professor Latto. It was not uncommon for people to have bugs living among their many layers of clothes like that clergyman they buried. Second, because if the fleas on humans carried the disease, the rats would not have had to do any travelling, they only had to infect fleas who were then whisked off by people as they travelled. I thought this was super interesting so if you want to read more, here’s the link:

Herd Immunity for Cerivical Cancer by HPV

When we went over herd immunity in class i was instantly intrigued, and it seemed to make a lot of sense, but i was thinking about it and i got a little bit curious what the percentage of the population would have to be vaccinated against the strains of Human Papillomavirus(HPV) that we have vaccines for until those strains were eliminated from the population via herd immunity. This is especially important when you consider that these two strains of HPV account for over 70% of cervical cancer from HPV.

Although countless hours of scientific journal research did not give me a percentage, it did lead to an interesting model that was made before the HPV vaccine that predicts the correlation of a HPV vaccine and the effects it would have on the number of cases of Cervical Cancer. The model assumed a 90% efficacy (the current vaccine is ~100%)with 70% of girls getting it at the age of 12. This study found the vaccine would decrease the overall HPV infection by 95.4%. It also found that cervical cancer would decrease by 61.8%. Keep in mind, this is only vaccinating girls, and they made a model for the vaccination o both boys and girls, but the boys results were largely insignificant in comparison.
So in terms of eliminating HPV entirely through herd immunity, i would estimate, that it would be between 70-80% of the would population would have to be vaccinated to eliminate the two strains of HPV that we currently have a vaccine for.



I mentioned in the first class that there were a number of different ways to classify diseases. We have generally been classifying and thinking about infectious diseases in terms of their causative agents.

However for many doctors, presented with a patient with an array of symptoms, it makes more sense to, at least initially, describe diseases according to their symptoms.

Pneumonia is an example of this someone raised in a question in the last class. Pneumonia is an inflammation of the lungs and can result from a wide variety of causes including bacteria, viruses, fungi, parasites and even non-biological sources such as dust.

Pneuomonia is actually an exception to the rule that the suffix -itis is used to indicate a disease marked by inflammation. You have probably heard of bronchitis, cystitis, laryngitis, meningitis, hepatitis etc - all of which name diseases that can be caused by a variety of organisms. In many cases knowing which organism is causing the disease is a vital next step.

Because of this association between the suffix -itis and disease people have sometimes coined words with it. The most common example being senioritis - taking it easy your senior year of high school. However, technically senioritis would refer to a swelling or inflammation of your seniors....

Saturday, January 30, 2010

We're going to need some crystals...

This might be a bit tangential to class but hey, that's what the blog is for. A number of times recently I have noticed a tendency of people to criticize science (sometimes 'mainstream science' or 'traditional science') as being very inflexible and unwilling to change whereas the alternative is the one portrayed as open to change. You often see this in the debate over 'alternative medicine'.

In reality the truth is pretty much the exact opposite. Science is remarkably open to new ideas. BUT what science does is to test those ideas. That's really all science is - a way of organizing our knowledge by proposing and systematically testing different ideas. Those ideas that don't work are eventually rejected (flat earth, miasma, witchcraft etc) and those that do work (germ theory etc) get increasingly refined and sometimes completely replaced by a whole new paradigm (Newton to Einstein etc). In many ways science is ALL ABOUT change. A career in science is not a good idea if you don't like change.

Most scientists are not against 'alternative medicine' because it is outside the mainstream - they are against it because it has been tested and there's little evidence it works. So why do many people believe in it? Because the placebo effect is HUGE. People DO improve if you give them a pill, potion, wave a magic wand, or stick needles in them - but only because they believe they will. This is also a problem with much traditional medicine. Many anti-depressant medicines (one of the most prescribed drugs) show only marginal improvement over a placebo.

Scientists have repeatedly tested many alternative 'therapies' and in cases where there appears to be some evidence of an effect (eg acupuncture) you'll find a fairly rich literature (in acupuncture though it is hard to rule out the placebo effect). In cases where there are good studies demonstrating no effect scientists tend to lose interest (eg homeopathy).

So I'm not sure why scientists, who have tested many if not all these 'therapies' are portrayed as being unwilling to change when advocates of pseudoscience like homeopathy, astrology or the notoriously litigious scientology persist in their beliefs even as evidence accumulates that their beliefs are wrong.

Friday, January 29, 2010

A Decade of Vaccines?

Hot off the press, well hot off the internets at least is news that Bill Gates is giving $10 billion to a ten year program focussing on vaccines for a variety of diseases. That's ten BILLION not ten million. The Gates foundation have a nice page on vaccines and their hopes for a 'decade of vaccines'.

Davos, Switzerland (CNN) -- Bill and Melinda Gates announced plans Friday to invest $10 billion in the fight against a number of illnesses including AIDS and said the record donation could save nearly nine million lives.

Speaking at the World Economic Forum in Davos, Switzerland, they said the 10-year program will focus on vaccines for AIDS, tuberculosis, rota virus and pneumonia.

"We must make this the decade of vaccines," said Bill Gates.

"Vaccines are a miracle," added Melinda Gates. "With just a few doses, they can prevent deadly diseases for a lifetime. We've made vaccines our priority at the Gates Foundation because we've seen firsthand their incredible impact on children's lives."

Thursday, January 28, 2010

S Z R Models

I introduced the basic SIR model for a simple epidemic to you. this model actually has a long history and was first described by Kermack and McKendrick in 1927.

As I indicated this model has since been expanded to include virtually every disease scenario you can imagine.

Last year a group of Canadian mathematicians used this SIR format as the basis for an analysis of a zombie epidemic. Their paper: WHEN ZOMBIES ATTACK!: MATHEMATICAL MODELLING OF AN OUTBREAK OF ZOMBIE INFECTION ) - somehow it seemed appropriate to keep that in capitals) - describes a model that should look basically familiar to you.

Notice in their S Z R model (Z for Zombie of course) there are two extra transitions - from R back to Z (reanimation of the dead is well established in the zombie movie genre) and a movement directly from S to R (non zombie related death).

This is, perhaps unsurprisingly, the first mathematical analysis of an outbreak of zombie infection. While the scenarios considered are obviously not realistic, it is nevertheless instructive to develop mathematical models for an unusual outbreak. This demonstrates the flexibility of mathematical modelling and shows how modelling can respond to a wide variety of challenges in ‘biology’.

In summary, a zombie outbreak is likely to lead to the collapse of civilisation, unless it is dealt with quickly. While aggressive quarantine may contain the epidemic, or a cure may lead to coexistence of humans and zombies, the most effective way to contain the rise of the undead is to hit hard and hit often. As seen in the movies, it is imperative that zombies are dealt with quickly, or else we are all in a great deal of trouble.

Wednesday, January 27, 2010

From 1400 to 1700, the Great Vowel Shift (GVS) changed the way people spoke English. As shown in the table below, long vowels were being pronounced using a different area of your mouth causing common words to sound completely different. And how, you ask, do we know about the GVS and the change in the articulation and sound of the English language? The ‘spelling errors’ found in old English books, rhyme schemes used by poets from this time, and early dictionaries that described how specific words were pronounced have allowed today’s historians to become aware of the GVS. To read more about the GVS visit







RP today

how, house




@U à aU
















oU, @U





@I à aI





















E; à e;



Plagues in Art

Artwork gives a strong visual description of the devastation plagues can cause in a region. These paintings reflect the pain and suffering that occurred as a result of the plagues.

To see more artwork of the plague :

MRSA and pets

Now you have to worry about getting MRSA from your dog.

Bring out yer dead

Why it's good to be King.

Tuesday, January 26, 2010

Black Plague and Miasma

Despite various efforts by church and government authorities to calm peoples nerves and assure them that all precautions were taken to keep everyone health, the plague (or a another deadly bacterium that causes swelling of the lymph nodes) swept through Europe with devastating effects in the 14th century. As people saw government officials, medical workers, and members of the clergy perish, they tried to find their own ways to stay ‘plague-free’. During the middle ages, the miasma theory was the leading explanation for the cause and spread of illnesses. Those who were still living used strong, and often putrid, scents to ward away the evil smell that carried the plague. In addition to sniffing pine, sulfur, and lemons, another ‘remedy’ thought to prevent the plague was loud sounds. Church bells rang in all towns, cannons were fired, and any mechanism that could cause loud noises was used to ward off the disease.

However, while these methods did nothing to prevent the deadly plague from ravaging towns, there were some methods used that were effective in preventing the coming Black Death. City officials in Milan sealed up houses that harbored someone with the plague, Venice forced all incoming ships to dock in a remote island, and, even though it was not known at the time that the plague bacterium is killed by heat, Pope Clement VI only breathed ‘pure air’ by sitting between large fires, effectively killing any plague bacteria. To read more about various precautions that were taken to prevent the plague see,

In 2003 New Scientist magazine reported on the contradictory results produced by a French and a British lab looking for evidence of Yersinia pestis DNA from plague corpses:
Case reopens on black death cause
The case remains far from solved. Until we dig up some more corpses.....

"If I can get some soft tissue from the plague, I'll look again," he says. In Finland, for example, there may be victims buried in permafrost.

Monday, January 25, 2010

Sweating Sickness

The Showtime series The Tudors is not exactly historically accurate (the Netflix description is 'historically loose but visually lush') but it does incorporate numerous real historical events and people.

In the first series a number of characters die from the 'sweating sickness'. This disease is real and its causative agent is still debated. It had a very rapid onset and its victims could be dead within a few hours following a very high fever.

A 1998 paper suggested that this disease might have been a Hantavirus although others remain unconvinced.

Like Bubonic Plague there is no doubt that a devastating and rapidly fatal illness did appear in England in the late 1400's and early 1500's but in this case it is even more mysterious. The disease was last seen in England in 1578.

Incidentally the Tudors is inaccurate in ascribing the death of Henry's bastard son to the sweating sickness at the age of 5. In real life he died of Tuberculosis at the age of 17. (I'm guessing they did this to foreshadow the later appearance of the disease). However, and I can't remember if they mention this or not, Henry's older brother (Arthur) did die of the sweating sickness at the age of 15. It was Arthur's widow (Catherine of Aragon) that Henry then takes as his first wife to maintain the alliance with Spain. It is then the inability of Catherine to give Henry the son he desires that leads to the whole rest of the saga (the six wives, the two beheadings etc etc).

So without the sweating sickness Henry would not have been king, England would not have broken from the Catholic Church and pretty much the rest of English and European history would have been different.


Sunday, January 24, 2010


I mentioned that ticks feed on birds and that birds can be hosts for Lyme disease. Although birds may not be either the preferred host for the ticks nor the most competent host for the ticks they may play a vital role in the story because they are so mobile.

Birds can both carry the ticks with them as they fly and also if the bird is infected with the Lyme bacteria in one location the bird's blood can spread the bacteria to the ticks in a new location

A team led by School of Public Health researcher Maria Diuk-Wasser analyzed studies on 71 bird species that host the black legged tick, the main carrier of Lyme disease. They found that 58.6 percent of the bird species can infect the tick with the bacterium that is responsible for Lyme disease. The literature review was published online in December in the journal Frontiers in Ecology and the Environment.

“Although it has been known for some time that birds play some role in Lyme disease epidemiology, this study integrates all the available information and points at particular bird species that may have a critical role in dispersing the Lyme agent,” Diuk-Wasser said.

Lingering Questions and Problems with Bolivian Hemorrhagic Fever (Machupo Virus) and Lassa Fever, Olivia Cvitanic

Both Bolivian Hemorrhagic Fever and Lassa Fever are viruses characterized as Arenaviridae and both are considered viral hemorrhagic fevers. Like Professor Latto discussed in class, humans normally Bolivian Hemorrhagic Fever because of mice who serve as asymptotic vectors. This also proves true for Lassa Fever as discussed in The Coming Plague where one species of field mice were infected villagers in West Africa. Humans get sick from contact with mice urine and excrement, saliva, or any other secretions. Also, some village people became infected through handling the mice before cooking them for consumption. However, there is some concern that the puzzle is not so simple and is certainly not complete for two reasons. First, the dominating treatment for both these viruses is an antiviral drug ribavirin which is most effective when the virus is diagnosed and treated at an early stage which is problematic especially in Africa where doctors and the drugs needed to treat patients are scarce and often too expensive. This is also bad because both these viruses can be transmitted from person to person. Secondly, there is still some confusion about the origins of these viruses. The incidences of the disease and the habitat of the mouse species in each instance doesn’t completely correlate and it has been suggested that this discrepancy may be the result of some amount of natural immunity among certain villages. However, as demonstrated in The Coming Plague, injecting an infected person with antibodies for the disease is only effective if the virus is caught early enough and, in the case of Lassa fever, if the antibody donor had the same strain of the virus. If you would like read more, here are the links to to the websites that got some of my information from:

Saturday, January 23, 2010

Under Our Skin again

Someone posted on this movie, Under Our Skin, last year when the movie was just released. It looks like it is getting another push for Oscar season. It's on the shortlist of 15 films for the Best Documentary Feature Oscar.
The topic of chronic long term lyme disease, or post lyme disease syndrome is one I didn't really have time to get into in class. It's an interesting topic.

A gripping tale of microbes, medicine & money UNDER OUR SKIN exposes the hidden story of Lyme disease, one of the most controversial and fastest growing epidemics of our time. Each year, thousands go undiagnosed or misdiagnosed, often told that their symptoms are "all in their head." Following the stories of patients and physicians fighting for their lives and livelihoods, the film brings into focus a haunting picture of the health care system and a medical establishment all too willing to put profits ahead of patients.

Friday, January 22, 2010

Bolivian Hemorrhagic Fever

So a little bit on the Bolivian Hemorrhagic Fever(BHF) that was mentioned today, as well as detailed in the first chapter of the book.
This disease is a little bit different from all the others that we have studied so far in that it is actually a viral infection as opposed to a bacterial one. and rather than a mode of transmission that requires ingestion of the pathogen, the BHF virus merely needs to be inhaled. Furthermore, this virus can be spread directly from one person to the next, although it is a rare occurrence.
relatively slow symptoms and a longer incubation period make the BHF, a result of the Machupo virus, difficult to detect due to it ambiguous early symptoms. The early symptoms can include fever, headaches, nausea, vomiting, anorexia, and muscular pain. Vomiting blood and nose bleeds follow, chased by dehydration and higher blood pressure(like Cholera). As the infection progresses, blood spots start to appear on the upper body while the nose, gums, stomach and intestine begin to bleed, which can lead to severe blood loss and hypotensive shock and neurological damage. In all, the disease has a mortality rate that ranges anywhere from 5-30%.

Due to the mortality rate, and the mode of infection, the Machupo Virus is rated at a bio hazard level 4, the highest level. There is currently no definite cure and a vaccine is being borrowed from a similar disease that shows some positive effects, but there is none specifically for the Machupo virus. In any case, this is why it is at biohazard level 4, which means that a Hazmat suit and self contained oxygen are required for work on the virus, as well as multiple showers, airlocks, leading to vacuum rooms and ultra-violet light rooms that have been shown to kill the virus. Other pathogens that are at this level of risk include the briefly mentioned hantavirus, the Ebola virus, and the bird flu.

Ecological Success Stories

'In order to publicize the benefits of the science of ecology, the Ecological Society of America has two issues available that highlight how ecology and ecologists have had a direct impact on human health, the economy, or quality of life.'

These two success stories are (drum roll please):

Hantavirus and Lyme Disease

Thursday, January 21, 2010

The Problems with Lyme Disease Tests-Olivia Cvitanic

In lecture, Professor Latto talked a lot about the symptoms of Lyme disease, how we contract the disease, and why we often don’t notice we’ve been bitten, no that is not a new freckle but a tiny nymph deer tick, duh. However, Professor Latto did not discuss the types of tests for people who may be infected. There are two tests that are most commonly used: ELISA and The Western Blot test. It’s sort of a two-pronged approach because only if you test positive on the ELISA test do you then undergo the Western Blot test. On average, the total cost of testing is usually between $25-$70.

The ELISA test analyses a person’s blood to detect the presence of antibodies against the Lyme disease causing bacteria Borrelia burgdorferi. If the test results come back positive or unclear for the ELISA test then a second test, the Western Blot test, is done to confirm the presence of the bacteria. However, it’s not all that simple according to doctors in the International Lyme and Disease Associated Society. Apparently, the tests will not come back positive for the bacteria antibodies if a person has recently, as in two weeks before or less, been bitten by an infected tick., resulting in a “false negative” test result. Due to the tests’ low sensitivity, many infected people assume they don’t have Lyme disease and leave the doctor’s office only to become ill as time goes on- thus getting tested may not save from experiencing some of the serious effects of Lyme disease.

If you would like to read more, I got my information from these two articles:

Lyme Disease in Man's Best Friend

In response to Professor Latto’s post about Lyme disease vaccinations for dogs, I researched how Lyme disease differs in humans and dogs. I found that only ten percent of dogs become infected if ticks carrying B. burgdorferi bite them. In fact, if infected ticks are found and removed from dogs within 48 hours, the bacteria will not be transmitted from the tick to the dog. In the case that dogs are infected with Lyme disease, their symptoms are different from humans and take longer to appear. After they are bitten and infected, it can from 2 to 5 months for dogs to fall ill and they do not develop characteristic rashes like humans. Rather the typical symptoms of Lyme disease in dogs include high temperatures (103-105 degrees), joint and lymph node swelling, little appetite, and they often become lethargic. Lyme disease is usually easily and effectively treated with penicillin-based antibiotics. However, in some of the worst cases, where dogs kidneys become infected, Lyme disease is very difficult to treat and can be lethal. Fortunately though, tick controls and vaccines are available to help prevent Lyme disease in canines.

For further information about Lyme disease in dogs as well as other animals, see

Chronic Lyme Disease

They want ta' legislate the moon
They want ta' legislate the womb
They wanna legislate all the things they hate
They want ta' legislate this tune

Hmm, Whatever happened to Grant Lee Buffalo? Ahh, they broke up in 1999 (thank you Wikipedia) - that explains why they've been quiet.

Anyhow, that brings us to today's topic - should we legislate what are essentially medical issue? Connecticut thinks so. In July last year House Bill 6200 passed through the Connecticut House of Representatives by unanimous approval (137 for, 0 against). What does this bill do? It protect Connecticut licensed Lyme treating physicians from prosecution by the State of Connecticut Medical Examining Board solely on the basis of a clinical diagnosis and /or for treatment of long-term Lyme disease - thus allowing them to provide long term antibiotic treatment for people with chronic lyme disease (and also sufferers from Post-Lyme disease syndrome).

Sounds reasonable? Except that in patients who have non-specific symptoms after being treated for Lyme disease, and no evidence of active infection (so called Post-Lyme disease syndrome or PLDS), studies have shown that more antibiotic therapy is not helpful and can be dangerous.
Read this report from the National Institute of Allergy and Infectious Disease (part of NIH). Read this letter regarding the bill sent by the Infectious Disease society of America.

I write on behalf of the Infectious Diseases Society of America (IDSA) to urge you to oppose the enactment of Connecticut House Bill No. 5625, which sanctions the use of long-term antibiotic therapy to treat Lyme disease and would protect physicians, who administer such therapies, from disciplinary action. In urging your opposition to this legislation, our primary concern is to ensure the best quality in patient care and to protect the public’s health and safety. To this end, we believe it is critically important that you be fully apprised of the widespread consensus within the medical and scientific community about the appropriate treatment of Lyme disease, as well as the medical community’s concerns about unproven, potentially harmful treatments for so called “chronic” Lyme disease that are advocated by a small group of physicians.
Carefully designed and conducted studies of Lyme disease treatments have failed to demonstrate benefit from prolonged antibiotic therapy. Rather, these studies have demonstrated that there is no difference in the measured improvement between patients receiving placebo and patients treated with antibiotics.

Furthermore, the scientific evidence that long-term antibiotic therapy may be dangerous, leading to potentially fatal infections in the bloodstream as a result of intravenous treatment. Far from improving the patient’s quality of life, prolonged antibiotic therapy may actually increase the patient’s suffering. Also, although the bacteria that causes Lyme disease does not acquire resistance to antibiotics, long-term antibiotic exposure can lead to drug-resistance among other microorganisms, creating “superbugs” that cannot be treated with currently available drugs.

I think we can expect to see more bills like this. It is the government's job to protect us from those who offer false hope and possibly dangerous 'cures' not to enable them.

Wednesday, January 20, 2010

Lyme vaccine? Yes and no....

I should have remembered this in class but as soon as I looked it up I remembered this story.

There IS a vaccine for Lyme disease - it is called Lymerix and conferred immunity to Borrelia in 76% of adults and 100% of children with only mild or moderate adverse effects. It was approved by the FDA in 1998.

However a number of class-action lawsuits were filed against GlaxoSmithKline alleging that the vaccine had caused health problems. Curiously these health problems were similar to those that are now being attributed to long term Lyme disease.

These claims were investigated by the FDA and the CDC, who found no connection between the vaccine and the autoimmune complaints however the damage was done and sales plummeted and the vaccine was withdrawn from the market by GalxoSmithKline in 2002.

The story is addressed in this 2006 News Story in Nature: Lyme disease: Uphill Struggle
The first vaccine against Lyme disease was withdrawn because patients distrusted it. Should market forces be allowed to shape the next one?
and in an accompanying editorial
When a vaccine is safe.
Unfounded public fears place pressures on vaccine developers that go beyond reasonable safety considerations, as the search for an acceptable vaccine against Lyme disease may demonstrate.

We will have more to say about vaccines - and the public attitude to them in future lectures. Meanwhile you can still get a Lyme Disease vaccine - but only for your dog.

Tuesday, January 19, 2010

Reading for this Weeks Section

This week will be reading a paper from Scientific American on the the evolution of virulence. You should have received the paper via email, but I've also posted it in the links section. Those of you in the Monday section who can't attend another section this week should complete the worksheet and turn it in next week.

Raising chickens

Now that consumers are willing to pay extra for food that is perceived to be organic or pesticide free there is also, thankfully, some interest in meat that is raised without the use of antibiotics. (Technically we should really just avoid the use of antibiotics as growth stimulators - their veterinary use should remain).

What is the poor meat producing industry supposed to do? Tyson Foods had a good idea - they would label their meat as 'raised without antibiotics' to attract the discerning shopper whilst continuing to inject eggs with antibiotics. Their argument - that the labels were accurate because chickens aren't "raised" until after they're born - didn't impress a judge and the company, although not admitting any wrongdoing, has agreed to settle the class action lawsuit for $5 million, not including $3 million in attorneys' fees.

Monday, January 18, 2010

Antibiotic Resistance and Obesity, Olivia Cvitanic

In class, we have talked a lot about drug resistant diseases and the effectiveness of antibiotics in our modern world. In this vein, many doctors worry about keeping antibiotics as a viable treatment option by prescribing it correctly in terms of type of antibiotics needed as well as the correct dose amount. Apparently, doctors are increasingly worried that their obese or very overweight patients are not being prescribed sufficient doses of antibiotics. According to Dr. Gurley, the author, antibiotics doses are not a “one size fits all” matter. In fact, obese people could become breeding grounds for heartier bacteria strains who are able to survive and reproduce because the antibiotic dose was not large enough to kill all of the bacteria. As obesity becomes a bigger problem in highly industrialized, developed nations where most of antibiotics are prescribed, the possibility that our antibiotics could be rendered less effective by not taking into account a person’s body weight is alarming and should be a subject of concern in the medical community. It would truly be a shame if humans were intelligent enough to develop antibiotics but more rapidly rendered them obsolete for failure to do some relatively simple math in prescribing them.

However many drug companies and doctors say it’s not that simple. The “kicker” according to Dr. Gurley is that changing the dose sizes and even pill sizes to appropriately accommodate people leaves drug companies a golden opportunity to “price-gouge” consumers. Should obese people be penalized financially for needing a larger dose of medicine? If so, then, Dr. Gurley argues, why not penalize people for their cardiac output or liver functions? I’m not sure how I feel about charging or not charging patients extra due to their weight, but I do think it’s an interesting point and a very serious point because if sick, obese people are not effectively treated then they could very well pass on drug resistant strains of antibiotics. If you are interested in the reading more, here’s the link:


The World Health Organization (WHO - an agency of the United Nations) has put out a public health risk assessment for Haiti.
Public health risk assessment and interventions: Earthquake - Haiti

It makes for interesting, and fairly depressing, reading with a lot of connections to the class. Did you know:
  • Cholera is not endemic in Haiti and will hopefully not be a problem. However, disruption of usual water sources and contamination of water by damaged sewage infrastructure may result in unsafe drinking water being consumed, increasing the risk of exposure to diseases such as typhoid fever and hepatitis A (Hepatitis A is a liver infection caused by the hepatitis A virus (HAV), and transmitted by the fecal-oral route.)
  • Risk of wound infection and tetanus are high due to the difficulties with immediate access to health facilities and delayed presentation of acute injuries. Gangrene is a complication of wound contamination, and prompt wound treatment is critical for its prevention.
  • Haiti has the highest TB incidence in the western hemisphere. In 2007, the estimated number of TB cases was 35 000 with an incidence of 147 cases per 100 000 population.
    The estimated prevalence of multi-drug resistant TB (MDR) among all new cases is 1.8%. It is likely that the treatment of thousands of TB patients will be interrupted - approximately 4 000 TB patients were undergoing treatment in Port au Prince alone.
  • Corpses do not represent a public health threat. When death is due to the initial impact of the event and not because of disease, dead bodies have not been associated with outbreaks. Standard infection control precautions are recommended for those managing corpses.

Sunday, January 17, 2010

Resistance genes in bear feces

Polar bears living in the pristine Svalbard area of Norway have a low diversity of bacteria in their feces, harboring mostly anaerobic bacteria from the genus Clostridia, and very few ampicillin resistance alleles.

"The presence of antibiotic resistance genes has previously been described in bacteria taken from the feces of deer, foxes, pigs, dogs and cats. The Barents Sea population of polar bears is located in an area that is sparsely populated by humans. This enables us to study an ecosystem with little human impact and should allow us to determine whether these genes are naturally occurring or are caused by exposure to human antibiotics."

From the current edition of BMC MicBMC Microbiology 2010, 10:10
Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard

Also picked up by some news sources - eg Reuters

Negelcted Tropical Diseases

What diseases have the most devastating impact on developing countries? AIDS? Malaria? Maybe TB? These diseases are often associated with high mortality, but many people around the world must deal with chronic disease as well. Parasitic diseases such as cysticercosis, Chagas disease, trichomoniasis and toxocariasi, don't often kill the host, but cause malnutrition, deformities, and can delay intellectual development. A new article in Scientific American suggests that treating these neglected tropical diseases (NTDs) could be a big step in raising those effected out of poverty.

Friday, January 15, 2010

More on Oswaldo Juarez

There's a post just below about Oswaldo Juarez, a Peruvian student in the United States who appears to be the first case of Extremely Drug Resistant Tuberculosis or XXDR-TB to be found in the US.

Reading a variety of news reports I found several interesting features of this case.

Juarez first checked into a hospital in Fort Lauderdale where he underwent three months of treatment with little effect. Then in December 2007 he was sent to and checked in voluntarily at AG Holley, just south of West Palm Beach in Florida, described by the AP as "the nation's last-standing TB sanitarium, a quarantine hospital that is now managing new and virulent forms of the disease.

The reassuring part is that they cured him but the process wasn’t easy. It took 19 months, and a drug regimen that left Juarez throwing up and thinking about suicide. At first his treatment was like chemotherapy: he was given drugs intravenously three times a day, and took 30 pills a day. He often had to take them several times because they made him nauseous and he would vomit them back up again. Juarez was given high doses of drugs, including some not normally used to treat TB.

His treatment cost $500,000.

Ashkin, one of the country's leading experts on TB, said only a handful of cases of XXDR-TB are known to have existed in the world.

"This is the new class that people are not really talking too much about," said Ashkin, who described Juarez's case as "the future" of drug resistant infections like TB and other killer diseases.

Viral DNA in the Human Genome

A mentioned today in lecture, humans, unlike bacteria, don't normally take up DNA from the environment. However, viruses can incorporate their DNA into ours, and there is evidence of this happening many times in the human genome.

Thursday, January 14, 2010

Olivia Cvitanic:The First Case of Multidrug Resistant TB in America

The First Case of Multidrug Resistant TB in America

The first case of highly drug resistant TB, XXDR TB, was identified in Lantana, Florida in December 2009. 19 year old Oswaldo Juarez came from Peru to visit America and study English. He came down with a slight cough that slowly developed into full blown tuberculosis, which became apparent after he began coughing up mouthfuls of blood one night, Juarez claimed, “I’m dying…because when you cough up bloodl it’s something really bad.”

Indeed, it was bad. This type of TB is bad for Juarez and for the many people he could have infected before he went into the hospital and those he could infect during his time at the hospital. Doctors seem to be offering up nothing but dismal views for the future. Dr. David Ashkin, one of today’s leading experts of tuberculosis says “He [Juarez] really is the future… These are the ones we really fear because I’m not sure how to treat them.”

Tuberculosis is not the only disease that’s mutating to resist treatment making our medicines obsolete. Malaria and HIV are also developing drug resistance. In fact, 65,000 Americans died last year due to drug resistant diseases which, sadly, is only expected to increase. The overuse and inappropriate use of antibiotics is one major reason diseases have been allowed to mutate and thus have become invulnerable to many drugs that in the past worked extremely effectively. I’m sorry my post is such a downer, but still, it’s all important stuff. If you would like to read more from this article, here’s the link:

Deciphering Gram-positive vs. Gram-negative bacteria

Penicillin is only beneficial when it is administered to patients that are infected with gram-positive bacteria. But how can scientist determine which bacteria are gram positive versus those that are gram negative? The answer...The Gram Staining Procedure! Using two different dyes, this process is able to differentiate which bacteria are composed of 90% cell walls (gram positive) and those that are only made of 10% cell wall (gram negative).

After researching, I found that the Gram Staining Procedure goes as follows:

1. Flood the slide with Crystal Violet (the primary stain).

2. After 1 minute, rinse the slide with water.

3. Flood the slide with Iodine (Iodine is a mordant that binds with Crystal violet and is then unable to exit the Gram+ peptidoglycan cell wall.)

4. After 1 minute, rinse the slide with water.

5. Flood the slide with Acetone Alcohol. (Alcohol is a decolorizer that will remove the stain from the Gram-negative cells.)

6. After 10 or 15 seconds, rinse the slide with water. (Do not leave the decolorizer on too long or it may remove stain from the Gram-positive cells as well.)

7. Flood slide with Safrinin (the counter stain).

8. After 1 minute, rinse the slide with water.

9. Gently blot the slide dry. It is now ready to be viewed under oil immersion (1000x TM) with a bright-field compound microscope.

After this staining procedure, the Gram positive cells will appear purple, having retained the primary stain. The Gram negative cells will appear pink, having retained the counter stain after the primary stain was removed by the decolorizer.

Another reason not to chase that dragon...

You can get anthrax.

Saving not just lives...

A child bomb-victim receiving penicillin treatment by Ethel Gabain. Painted 1944 and part of the Imperial War Museum Collection it is currently part of an exhibit at the Canadian War Museum.

Gabain's image of the child being treated with penicillin shows her isolated, amid weights and levers and drips that balance and sustain her. However, the overall impression here is of someone safe, protected and, as she engages the viewer, hopeful. Penicillin saved her leg from amputation. This was one of a series of paintings commissioned to display scientific developments. Gabain had lost a child during the war and was herself in poor health when she undertook the commission.

It's important to remember that Penicillin saved not just lives but also numerous limbs which no longer needed to be severed to avoid the potentially fatal effects of infection. Not just in soldiers but in anyone who sustained serious (or sometimes not so serious) wounds from accidents, surgery or any of a dozen other causes.

Penicillin synthesis

A number of magazines and newspapers have now put most, if not all, of their archive material online. This means that Google searches now throw up original news reports from decades ago, way before the internet.

I was looking for some details about the development of synthetic penicillin and found this report from Time magazine in 1957 describing the discovery of the first practical method of synthesizing Penicillin. There's a nice description of why the problem was so hard:

The molecule is not unusually complicated, but extremely fragile. Any kind of rough treatment, such as heat or acids, makes it fall into fragments that cannot kill any kind of germ. To use the customary chemical methods on penicillin, says Dr. Sheehan, "would be like attempting to repair a fine watch with a blacksmith's sledge and anvil." The critical problem was to find a way to bond a carbon atom and a nitrogen atom to form a chemical ring in the heart of the molecule. Avoiding many standard reagents as too violent, and keeping his solutions at room temperature or lower, Dr. Sheehan finally found a reagent that would do the job.

Wednesday, January 13, 2010

Antibiotic Resistance

Antibiotic resistance is on the rise. Following the mass production of penicillin in 1943, microbes appeared that could resist the widespread antibiotic. Unfortunately, antibiotic resistance spreads fast. "Between 1979 and 1987, for example, only 0.02 percent of pneumococcus strains infecting a large number of patients surveyed by the national Centers for Disease Control and Prevention were penicillin-resistant. CDC's survey included 13 hospitals in 12 states. Today, 6.6 percent of pneumococcus strains are resistant, according to a report in the June 15, 1994, Journal of the American Medical Association by Robert F. Breiman, M.D., and colleagues at CDC. The agency also reports that in 1992, 13,300 hospital patients died of bacterial infections that were resistant to antibiotic treatment."

Why such an increase in prevalence? Antibiotic resistance is the result of evolution. The natural variant with the ability to withstand an antibiotic's attack on a microbe has been favorably chosen by natural selection.

Although antibiotic resistance is a natural process, there are other factors contributing to the rise. These factors include: increased infection transmission as well as inappropriate antibiotic use.

What is there to fear? According to a report in the April 28, 1994, New England Journal of Medicine, researchers have identified bacteria in patient samples that "resist all currently available antibiotic drugs." While antibiotic resistance is inevitable, the process can be slowed through improving infection control, developing new antibiotics, and using drugs more appropriately.

To read more about The Rise of Antibiotic Resistance: