Friday, February 29, 2008
To watch the video: Click Here.
Canada confirmed a new case of mad cow disease on Tuesday, the 12th. The animal in question was a six-year-old dairy cow from Alberta that had most probably eaten infected feed. The Canadian Food Inspection Agency, which vows to eradicate bovine spongiform encephalopathy (BSE) within a decade, has consistently said it expects to find a few cases of the disease. The CFIA said no part of the animal had entered the human or animal food supply. The cow was born after Canada and the United States introduced a ban in 1997 on cattle feed that contained ingredients made from rendered cattle and other ruminants. At least four other cases have involved animals born after 1997. "Many trading partners in the past have shut their borders to Canadian cattle and beef products after the first home-grown case in 2003, dealing a massive blow to the industry, and Ottawa has fought hard to restore market confidence. Last May the World Organization for Animal Health relaxed its security rating on both the United States and Canada, classifying both nations as controlled risk in a sign it was happy with their efforts to combat BSE. "This case will not affect Canada's controlled risk country status," the CFIA said in a statement. "Based on science, it is not expected that this case should impact access to any of Canada's current international markets for cattle and beef." Mexico noted last Friday that it would soon lift a ban on Canadian cattle imports that dated back to 2003. Here's the link to the article.
Terrorists have also utilized zoonotic agents as a means of weaponry. Although biological weapons are much more complicated and dangerous to deal with than typical terrorist bombs, the immense consequences that they are capable of producing make them appealing. Not until recently has the United States instituted programs to confront the growing threat of biological warfare. The response to such weapons includes advancements in the physical protection of soldiers against bio agents, monitoring research programs around the world, and participating in many large scale treaties. For more: Click Here
Thursday, February 28, 2008
This past December, not too long before the Christmas holiday, 49 people being held in a facility near Port Elizabeth, South Africa cut through a perimeter fence and escaped. These people weren't criminals locked away in a prison; they were patients at the Jose Pearson Hospital diagnosed with highly infectious, drug-resistant tuberculosis.
The use of mandatory isolation to keep disease such as tuberculosis in check is a centuries-old practice. Isolating people with confirmed or suspected infection has helped protect the public from diseases such as smallpox and, more recently, severe acute respiratory syndrome (SARS). A newly published review of 51 studies has found that physical barriers work better than drugs at preventing the spread of respiratory viruses
You will need to be on a campus computer or use the library proxy to access the Nature and British Medical Journal links directly.
I think this is one of those problems that we could fix with appropriate investment and effort. The problem is, as the report highlights, that we are not putting in the necessary investment:
WHO estimates that US$4.8 billion is needed for overall TB control in low- and middle-income countries in 2008, with US$1 billion for MDR-TB and XDR-TB. But there is a total financing gap of $2.5 billion, including a US$ 500 million gap for MDR-TB and XDR-TB.
Not investing the money to fix these problems now could get very expensive in the long run. Wired magazine asked WHO's 'Stop TB program' director Mario Raviglione why the US should be concerned about XDR-TB given that there4 have only been 49 cases here to date:
Even a couple cases a year costs the U.S. system tremendously. It costs several hundred thousand dollars to treat a case; they might need to have surgery, and the cost of drugs is tremendously high, as is the cost of following that person to make sure they're taking the drugs. Even a few casses a year is a very costly exercise. The best thing is to prevent MDR-TB and XDR-TB.
A billion dollars or two is a very small fraction of the federal budget - this is the sort of money politicians regularly lose down the back of the sofa. We should see spending on controlling drug resistant TB as an investment in the future.
Wednesday, February 27, 2008
Tuesday, February 26, 2008
Bacteria Show Promise In Fending Off Global Amphibian Killer - (May 25, 2007) — First in a petri dish and now on live salamanders, probiotic bacteria seem to repel a deadly fungus being blamed for worldwide amphibian deaths and even extinctions.
Parasites Might Spur Evolution Of Strange Amphibian Breeding Habits Parasites can decimate amphibian populations, but one researcher believes they might also play a role in spurring the evolution of new and sometimes bizarre breeding
Monday, February 25, 2008
Andrea Swei, a grad student in my wife's lab who actually works on the Lyme disease project, wrote this summary of the chytridiomycosis project for the Berkeley Science Review. You heard much of this story today, how would you have summarized it - what would you have left in and taken out?
Sunday, February 24, 2008
The technique uses gold nanoparticles coated with a sugar and a protein that binds to sugars. Meanwhile, a variety of antibiotics are placed in the same solution. A spectrophotometer reads optical variations in the gold nanoparticle solution as the sugar and protein shift , which in turn demonstrate which antibiotics effectively halt bacteria growth and which ones do not. Results can be obtained within a couple of hours, in contrast to the traditional methods, which can take days to complete. And hundreds of samples can be tested at once using this technique because the amount of bacteria and antibiotic needed is small.
The research paper is published in the journal 'Analytical Chemistry' but there is a summary here.
Saturday, February 23, 2008
Friday, February 22, 2008
While searching for some interesting articles about toxoplasmosis I was amazed by the range of effects of latent toxoplasmosis that various studies have claimed to find. Increased risk in traffic accidents, higher levels of intelligence, decreases in body weight, and lower guilt proneness are just a few of the many effects of dormant toxoplasmosis which I saw on just one google search! The subjective nature of some of these results, the lack of cause and effect evidence, and the fact that such a huge portion of the population is infected with latent forms of toxoplasmosis leads me to believe that some of these experiments may be trying to make something out of nothing...but that's just me.
Thursday, February 21, 2008
To prevent risk of toxoplasmosis and other infections from food:
- Cook food to safe temperatures. A food thermometer should be used to measure the internal temperature of cooked meat. Do not sample meat until it is cooked.
- Beef, lamb, and veal roasts and steaks should be cooked to at least 145°F throughout.
- Pork, ground meat, and wild game should be cooked to 160°F.
- Whole poultry should be cooked to 180°F in the thigh.
- Peel or wash fruits and vegetables thoroughly before eating.
Photo courtesy of USDA.
- Wash cutting boards, dishes, counters, utensils, and hands with hot soapy water after contact with raw meat, poultry, seafood, or unwashed fruits or vegetables.
- Freeze meat for several days before cooking to greatly reduce chance of infection.
To prevent risk of toxoplasmosis from the environment:
- Avoid drinking untreated drinking water, particularly when traveling in less developed countries.
- Wear gloves when gardening and during any contact with soil or sand because it might be contaminated with cat feces that contain Toxoplasma. Wash hands thoroughly after gardening or contact with soil or sand.
- Keep outdoor sandboxes covered.
- Feed cats only canned or dried commercial food or well-cooked table food, not raw or undercooked meats.
- Change the litter box daily If you own a cat. The Toxoplasma parasite does not become infectious until 1 to 5 days after it is shed in a cat's feces. If you are pregnant or immunocompromised:
- Avoid changing cat litter if possible. If no one else can perform the task, wear disposable gloves and wash your hands thoroughly with soap and water afterwards.
- Keep cats indoors.
- Do not adopt or handle stray cats, especially kittens. Do not get a new cat while you are pregnant.
It was found that people exposed to toxoplasma had a 24% higher risk of developing schizophrenia. Researchers did a study out of180 study individuals diagnosed with schizophrenia, 7 percent had been infected with toxoplasma prior to their diagnosis, compared to 5 percent among the 532 healthy recruits. The difference, while seemingly small, is important, researchers say, because the ability to explain even a small portion of the 2 million cases of schizophrenia in the United States may offer clues to the disease and some possible treatments. There have been previous studies reported on the link between schizophrenia and the presence of toxoplasma antibodies, which are evidence of past infection, but this is the first study to show that infection with the parasite can precede the initial onset of symptoms and subsequent diagnosis with schizophrenia. While most people infected with toxoplasma never develop schizophrenia, the parasite may be a trigger in those genetically predisposed to the disorder, a classic example of how genes and environment come together in the development of disease. Here's the link to the article.
MRSA: Mathematical Modeling Offers New Approaches To Fight Dual-resistant Hospital Infections
A mathematical model that looks at different strategies for curbing hospital-acquired infections suggests that antimicrobial cycling and patient isolation may be effective approaches when patients are harboring dual-resistant bacteria.
Changing The Way Antibiotics Are Prescribed May Be Key To Controlling Epidemics.
A sophisticated new mathematical model has identified what may be the key to getting this growing health problem under control: Changing the way that antibiotics are prescribed and administered.
Wednesday, February 20, 2008
Toxoplasmosis changing human behavior was reported on by the Times (archived here) and, more sensationally, by the Australian Sydney Morning Herald with the great headline 'Parasite makes men dumb, women sexy'.
For such an amazing result the Toxoplasmosis/traffic accident story was largely ignored by the press although the BBC did do a news story. The Czech traffic accident survey has now been repeated in Turkey with essentially the same result.
I don't quite know what to make of this one. Apparently women affected with Toxoplasmosis are more likely to have sons than daughters.
Tuesday, February 19, 2008
...until someone loses an eye.
From John's post about horrifying parasites, I found a link to a news video about a parasite which attacks unwitting contact-lens wearers. The name of the parasite sounded familiar, and being a contact wearer myself, I did some more research:
Acanthamoeba is a group of amoeba that are common in the environment, in soil and water. Some of them are pathogenic to humans, causing encephalitis when they enter wounds, or potential blindness when they enter the eyes. The video mentions that people have gotten such infections from contaminated water coming into contact with their contact lenses (such as musician Momus).
Many sources suggest that one could contract this parasite by wearing their contacts while swimming, surfing, etc. The risk in wearing contacts while swimming is that when the parasite gets between the lens and the eye, it is protected from removal by blinking action. The incidence is low (like 1.5 cases per million people per year in the U.S.), though contact-lens wearers are at higher risk. Thats a risk I'll have to take as I definitely need my contacts when surfing, but it is something to think about in relation to the public pool (and hot tubs). The literature suggests that cleaning lenses after swimming, throwing them out, or just not wearing them are the best prevention.
I also recalled some uproar about parasites in eyewash stations in science laboratories, so did a quick search and found a few articles mentioning that yes, acanthamoeba have been cultured from eye wash stations... (and this). A huge number of eye-wash stations seem to be sources of bacteria, amoeba, and fungi. But if they are cleaned/flushed regularly, this is much less of a problem. And again, preventive measures from getting nasty chemicals in one's eyes can reduce the risk of needing to use one in the first place.
Refer to wikipedia article for a teaser of how acanthamoeba might interact with MRSA.
Monday, February 18, 2008
As a prelude to the upcoming week's lectures here is a video inspired by an article on horrifying parasites. I should note that the video is more for amusement than scientific accuracy but if you've already watched it hopefully you figured that out. The video was created entirely from public domain footage from old b-movies, forgotten creature features and cheesy instructional films with a couple of title cards and the voice over being the only additions.
Sunday, February 17, 2008
Saturday, February 16, 2008
State health regulators approved a sweeping crackdown designed to stem the spread of infections inside hospitals, a crisis blamed for thousands of patient deaths and millions of dollars in unnecessary medical expenses. The Public Health Council voted unanimously to dispatch state inspectors regularly to hospitals to make sure they are following rules on preventing infections and reporting them promptly when they happen. The panel also approved a plan to issue report cards on infection rates for each hospital and to post that information on a state government website. A hospital that failed to comply with the rules or continued to have an excessive number of infections could potentially forfeit its license.
A state report last summer found that potentially lethal infections contracted during hospital stays could be responsible for up to $473 million in medical costs annually in Massachusetts, a reflection of extended hospital stays and medication and surgical costs. National studies estimate that up to 90,000 patients a year die because of infections they catch while in medical facilities, with deadly germs gaining entry through surgical incisions and catheters and sometimes transmitted by doctors and nurses who fail to wash their hands. Here is the link to this article by the Boston globe.
Risk factors for hospital-acquired (HA) MRSA include:
- A current or recent hospitalization. MRSA remains a concern in hospitals, where it can attack those most vulnerable — older adults and people with weakened immune systems, burns, surgical wounds or serious underlying health problems. A 2007 report from the Association for Professionals in Infection Control and Epidemiology estimates that 1.2 million hospital patients are infected with MRSA each year in the United States. They also estimate another 423,000 are colonized with it.
- Residing in a long-term care facility. MRSA is far more prevalent in these facilities than it is in hospitals. Carriers of MRSA have the ability to spread it, even if they're not sick themselves.
- Invasive devices. People who are on dialysis, are catheterized, or have feeding tubes or other invasive devices are at higher risk.
- Recent antibiotic use. Treatment with fluoroquinolones (ciprofloxacin, ofloxacin or levofloxacin) or cephalosporin antibiotics can increase the risk of HA-MRSA.
These are the main risk factors for community-acquired (CA) MRSA:
- Young age. CA-MRSA can be particularly dangerous in children. Often entering the body through a cut or scrape, MRSA can quickly cause a wide spread infection. Children may be susceptible because their immune systems aren't fully developed or they don't yet have antibodies to common germs. Children and young adults are also much more likely to develop dangerous forms of pneumonia than older people are.
- Participating in contact sports. CA-MRSA has crept into both amateur and professional sports teams. The bacteria spread easily through cuts and abrasions and skin-to-skin contact.
- Sharing towels or athletic equipment. Although few outbreaks have been reported in public gyms, CA-MRSA has spread among athletes sharing razors, towels, uniforms or equipment.
- Having a weakened immune system. People with weakened immune systems, including those living with HIV/AIDS, are more likely to have severe CA-MRSA infections.
- Living in crowded or unsanitary conditions. Outbreaks of CA-MRSA have occurred in military training camps and in American and European prisons.
- Association with health care workers. People who are in close contact with health care workers are at increased risk of serious staph infections.
Friday, February 15, 2008
Great question. The answer to this question (what percentage of people acquire HIV from sexual intercourse, through the sharing of needles, and by other means) will vary a lot depending on the time period you are asking about and the country you are asking about.
Let's look at a few examples.
According to the CDC, in 2005 the cumulative figures for the AIDS epidemic in the US were:
Male to male sexual contact - 48%
Intravenous drug use - 26%
Both Intravenous drug use and male to male sexual contact - 7%
Heterosexual sex - 17%
Other - 2%
The sample size here is almost a million people.
BUT in the year 2005 alone, the figures were:
Male to male sexual contact - 43%
Intravenous drug use - 20%
Both Intravenous drug use and male to male sexual contact - 5%
Heterosexual sex - 30%
Other - 1%
Spot the difference? Heterosexual transmission has almost doubled and now accounts for 30% of cases. The other figures have gone down accordingly.
The final example is Africa, where data is harder to come by but numerous sources suggest 80% of the HIV infections in Africa are due to heterosexual sex with mother to child (vertical) transmission accounting for most of the rest. This paper has further data on African and some other areas plus a few useful references.
Thursday, February 14, 2008
Risk and outcome of nosocomial Staphylococcus aureus bacteraemia in nasal carriers versus non-carriers
Published in the Lancet journal in 2004. This is so relevant I think I'll actually mention this one in class. The answer is that as a carrier you are three times more likely to get an infection but much less likely to die of an infection if you get one. Non carriers are thus less likely to get infected but more likely to die if they do get infected!
Wednesday, February 13, 2008
"If you go into an intensive care unit in a major Sydney hospital it is almost inevitable that you will get MRSA if you stay long enough."
Richard West, chair of the Royal Australasian College of Surgeons infection control advisory committee.
A google news search on MRSA will bring up several thousand articles.
It's painfully obvious that what we most need is a new acronym. Fortunately the CDC is available to bring us HA-MRSA: Healthcare-Associated Methicillin Resistant Staphylococcus aureus.
Tuesday, February 12, 2008
For more about TRIPs: CLICK HERE
The CDC position on sexual intra-human Borrelia burgdorferi (Bb) transmission is that it does not occur. We find no study that addresses sexual transmission of Bb among humans; conversely, we find no study supporting that it does not occur. Inferential data, however, suggest the possibility of human sexual transfer. The data come from sound veterinary studies, the finding of Bb in human semen and breast milk, and by similarity to Treponema pallidum where sexual transfer is abundantly documented. Our clinical experience strongly suggests that predictable, possibly inevitable Bb transfer between sexually active couples occurs.
From: Lyme disease': ancient engine of an unrecognized borreliosis pandemic?
W. T. Harvey, P. Salvato
Monday, February 11, 2008
Hot off the press is a news report that Ebola may not be so hard to work with in the future after all. By removing a single gene from the virus scientists were able to stop it replicating. That's one result they might want to double check......
Sunday, February 10, 2008
Popular Science magazine has an annual article on the worst jobs in science. Cherie mentioned that tick dragger made the list in their very first year. Their latest listing is here.
So, for Week 6, homework is to read Chapter 5.
For more 'background' on Ebola, check out the movie "Outbreak." It's fiction, and its not actually about Ebola (just an Ebola-like virus), but you are welcome to use this as an excuse to watch TV in the name of education. See if you recognize one of the characters from the sitcom "Friends."
I also highly recommend Richard Preston's non-fiction book "The Hot Zone," which is about Ebola and other hemorrhagic viruses. This book, and the aforementioned movie, were some of my favorites in high school.
Saturday, February 9, 2008
"I like to say it's like kissing everybody at the party — if you're double dipping, you're putting some of your bacteria in that dip."
Friday, February 8, 2008
I think the midterm went well. Tom and I managed to grade most of it today and we'll be able to get it finished on Monday so you'll get it back in section next week. If you have feedback on the format of the midterm then I'd love to hear it, the final will roll around before we know it.
Plus, we are now halfway through the course so if you have comments on the course then now would be a great time to pass them on. I do welcome and read all the feedback I get on the end of course evaluations but if you give me feedback before the course is over I may be able to improve the course for you.
Thursday, February 7, 2008
Wednesday, February 6, 2008
In the spring of 1996, as Atlanta prepared to host the summer Olympic Games, an outbreak of syphilis struck a group of teenagers in the prosperous bedroom community of Conyers, Georgia. When epidemiologists interviewed the victims, they were shocked by what they heard: children as young as fourteen named scores of sexual partners, others told of all-night orgies and sex parties.
I'm pretty unshockable but I found this PBS show on an outbreak of syphilis in Georgia pretty amazing. Although the show was aired in 1999, thanks to good old PBS you can access a lot of information about it at a website dedicated to the show and even read a complete transcript.
The website will also give you access to details about the actual investigation of the outbreak, the techniques used and the results. For example this paper shows the complete network visualization of the outbreak I presented in class.
I'm not clear who initiated this trend but many organizations are now using both STD/STI (eg American Social Health Association) some are sticking with STD (eg the Center for disease Control and Prevention) and some are just using STI (eg the World Health Organization)!
The terms are not synonymous, as Wikipedia points out:
'The term STI — which refers to infection with any germ that can cause an STD, even if the infected person has no symptoms — is a much broader term than STD. The distinction being made, however, is closer to that between a colonization and an infection, rather than between an infection and a disease.'
- All the questions on the midterm can be answered using material from lecture.
- Week 5 material is not included on the midterm - just the first 4 weeks.
- You do not need to bring a blue book or scantron.
- You do need to bring a pen and please, please write legibly.
- Use the glossary and terminology summary as a guide to the terms you need to know but you will also need to know concepts from lecture.
- The class grades may be curved - but only to your benefit. I'm quite happy for everyone to get an A grade and if that happens I will be delighted. On the other hand if everyone gets a C and, after consultation, it looks like this was my fault for being too tough I will set a curve.
Tuesday, February 5, 2008
My forgetters getting better
But my rememberer is broke.
To you that may seem funny,
but to me that is no joke.
For when I'm "here" I'm wondering
If I really should be "there"
And, when I try to think it through,
I haven't got a prayer!
Oft times I walk into a room,
Say "what am I here for?"
I wrack my brain, but all in vain
A zero, is my score.
At times I put something away
Where it is safe, but, Gee!
The person it is safest from
Is generally, me!
When shopping I may see someone,
Say "Hi" and have a chat,
Then, when the person walks away
I ask myself, "who's that?"
Yes, my forgetters getting better
While my rememberer is broke,
And it's driving me plumb crazy
And that isn't any joke.
The Mold in Dr. Florey's Coat by Eric Lax- an interesting account of the discovery and development of penicillin. It focuses on the people and gives you a good perspective on the difficulties they faced.
Disease in History by Frederick Cartwright - a little old now but really a classic text on the impact of disease on history.
The hot zone by Richard Preston. The dramatic and chilling story of an Ebola virus outbreak in a surburban Washington, D.C. laboratory. Richard Preston has also written a book about the potential use of smallpox as a biological weapon called The demon in the Freezer. I like the fact he got Stephen King to write a blurb for the back including this quote: 'One of the most horrifying things I've read in my whole life'.
The Ghost Map: The Story of London's Most Terrifying Epidemic--and How It Changed Science, Cities, and the Modern World by Steven Johnson. I think I already mentioned this one, a recent book discussing John Snow, Cholera and the origin of epidemiology.
Monday, February 4, 2008
This Worldmapper website re-sizes countries for each area of interest. In the picture above, the territory size represents the proportion of people infected with HIV living there. Use the worldmapper to check out everything from the amount of smoking men to the amount of Cholera cases to the amout of car accidents to the amount of hospital beds. It is a great site that is fun and interesting to fool around on so, go for it! Worldmapper Home
FYI the Isla Vista Medical Clinic at 970 Embarcadero Del Mar offers both Confidential and Anonymous HIV testing.
Sunday, February 3, 2008
The Centers for Disease Control and Prevention face a 7% cut of more than $430 million, including $27 million cut from its efforts to detect and control infectious diseases, and $28 million cut from chronic disease prevention and health promotion.
My math could be wrong here but it looks like the entire CDC budget (which must be around 6 billion if $430 million is 7% of it) is less than a fifth of the defense spending increase proposed for this year (the increase must be about $36 billion if it is 7% of $515 billion). It gets confusing when you have trillions, billions and millions in the same story....
'The height of reckless irresponsibility on the part of ABC and its parent company The Walt DisneyCo.'
Renee Jenkins, president of the American Academy of Pediatrics.
I didn't see it but ABC started a new show last week in which the storyline involved the hypothesis that autism is caused by a mercury-based preservative formerly used in common childhood vaccines. Despite the fact there is virtually no scientific data linking vaccines and autism and numerous studies have failed to find a link, the show treats the hypothesis as being credible and only presented a notice at the end to say "The preceding story is fictional and does not portray any actual persons, companies, products or events". The New York Times has an article about it.
Interesting issues here, do TV companies have moral obligations or are they simply beholden to their owners and/or shareholders? We have seen the effect of declining vaccine uptakes in other countries sparked by rumors so it would be naive to suggest that a TV show couldn't have an effect.