Summer reading 3: Good Germs, Bad Germs by Jessica Snyder Sachs

Balance is a tricky thing to find in area, and medicine is notorious for its trade-offs. A drug that may make you well in the long run may also have side effects that make taking the medicine difficult. Even drugs that we often think of as typically innocuous, such as antibiotics, can have an enormous cost associated with their use, both at the individual and the population level. Sachs covers our love-hate relationship with antibiotics and germs in general in her book, Good Germs, Bad Germs. More after the jump…
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Landscape ecology and infectious disease: macro meets micro

I spent all day yesterday in Madison, Wisconsin, at a conference on Landscape Ecology and infectious disease. I’ll discuss a few of the talks and issues below, but I wanted to start out with a bit of an introduction and explain just what landscape ecology (LE) is.

The introductory talk, which covered this ground, was presented by Dr. Michael Wimberly of South Dakota State University. He noted that defining LE wasn’t an easy task. At its most basic, of course, it’s a field looking at ecology from a landscape perspective–taking a big picture view, if you will. However, what one means by a “landscape” can vary widely. The landscape could be a few square feet of soil in a rainforest; it could be a village; or even an entire country or beyond. Whichever landscape one is looking at, it all boils down to scale, and LE methods can be used to move from one scale to another (e.g., from a village to a county to a state). These different levels of analysis are important not only for the traditional areas LE is used to study–examining ecological impacts of things like fire or climate change on forest ecology, for example–but are also becoming increasingly accepted in infectious disease modeling. More on that after the jump…
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On E. coli, super soil bacteria, and Hank Williams Jr.

Early this week, grant application; yesterday and today, IRB and IACUC for another project. But once again, fellow Sbers are keeping me busy reading about stories I’d like to be writing on; see yet again Mike on E. coli O157:H7–everything old is new again; Ed on a new study showing yet again how amazing bacteria are; and DrugMonkey discussing heroin addiction as a family legacy, and notes that this sad story again shows that Narcan saves lives.

The threat of emerging poxviruses: replacements for smallpox?

1980 marked a milestone in infectious disease epidemiology: the World Health Organization declared the smallpox virus eradicated in the wild. However, while smallpox currently exists only in frozen stocks, poxviruses as a class certainly haven’t disappeared. A related virus, monkeypox, regularly causes illness in Africa, and even spread half a world away in the American midwest.

Additionally, Africa isn’t the only area with endemic poxvirus infections. Brazil has been dealing with their own poxvirus outbreak, and poxviruses have popped up in Europe as well. More on both of those after the jump…
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What’s Google got to do with emerging diseases?

As I mentioned Friday, the good folks from Google were part of the crowd at this year’s ICEID. This included a talk by Larry Brilliant, described on his wikipedia page as “…medical doctor, epidemiologist, technologist, author and philanthropist, and the director of Google’s philanthropic arm Google.org.” His talk discussed not only stopping outbreaks in their tracks–as current outbreak investigations seek to do, and Brilliant himself as worked on, as part of his background in vaccination campaigns for polio and smallpox–but to pay attention to “the left of the epidemic curve” as part of Google’s “Predict and Prevent” initiative. More on what that means after the jump.
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Thar’s bacteria in that there snow!

I really need more time to fill in a gap in my microbiology education: environmental microbiology. I run across papers all the time that are absolutely fascinating, and wish I had a free year to just take some additional coursework in this area. For instance, a paper in today’s Science magazine discusses how atmospheric bacteria result in the formation of snow; more after the jump.
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Fecal transplants to cure Clostridium difficile infection

Blogging on Peer-Reviewed Research In my field, many things that cause the average man-on-the-street to get a bit squeamish or squicked are rather commonplace. My own studies include two types of bacteria that are carried rectally in humans (and other animals), so I spend an absurd amount of time thinking about, well, shit, and the lifeforms that inhabit it and collectively make up our normal gut flora. The vast majority of these species don’t harm us at all, and many are even beneficial: priming our immune system; assisting in digestion; and filling niches that could be colonized by their nastier bacterial brethren.

It’s typically when there’s some disturbance in these flora that bad things happen. For example, you may ingest food contaminated with a foreign bacterial strain that may transiently colonize your intestines, resulting in cramping and diarrhea. Typically these infections are self-limited and your normal flora “resets itself” after a short time, but some pathogenic bacteria have a propensity for making themselves at home in your gut. How to get rid of these nasty invaders then? Antibiotics are one option, but they also kill your regular bacteria, potentially making the problem worse (especially if the nasty invader happens to be resistant to many antibiotics). There has been a large increase in the use of probiotics–formulations designed to add beneficial bacteria to your gut. However, these have largely not been rigorously tested or regulated, so it’s unsure how well they actually work.

What if, instead of re-constitituing healthy gut flora one species at a time, you could simply take the entire fecal contents from a healthy person and use it to re-colonize your own gut–in other words, undergo a fecal transplant? Yes, it’s like probiotics on steroids: getting an infusion of someone else’s gut flora in order to re-establish a healthy gut ecology of your own, and squeeze out some potentially harmful organisms along the way. A recent story discusses this treatment for patients suffering Clostridium difficile infections in Scotland, but it’s actually not brand-new, and has already surfaced in the peer-reviewed literature. More after the jump…
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MRSA and swine: collision course

Blogging on Peer-Reviewed Research Both Mike and Revere have new posts up documenting swine as a new threat to human health (beyond the pork chops and bacon), via carriage of methicillin-resistant Staphylococcus aureus in these animals. Several papers have been published recently documenting high rates of MRSA carriage in swine in the Netherlands, and also have documented transmission of this bacterium from swine to humans. However, even more worrisome to me than the Dutch publications is a new one out in Veterinary Microbiology, showing high rates of MRSA in Canadian swine–and guess where we import about 9 million hogs from every year?

More after the jump…
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Bad science writing of the day: your gut bacteria make you crave chocolate

I’ve written a post or two (or a dozen) discussing science journalism–the good, the bad, and, mostly (because they’re the most fun), the ugly. There was this story about how blondes “evolved to win cavemen’s hearts.” Or this one that completely omitted the name of the pathogen they were writing about. Or this one, where a missing “of” completely changed the results being discussed.

I ran across another glaring example yesterday, dealing interestingly enough with one of my favorite topics: chocolate, and bringing in an “omics” prospective to it.
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Newly discovered Ebola viruses: filling in gaps in viral ecology

It’s only taken 30 years, but information about Ebola in nature is finally starting to snowball. First, after almost 15 years of disappearing from the human population, Ebola returned with a vengeance in the mid 1990s, causing illness in 6 separate outbreaks in Gabon, Ivory Coast, Democratic Republic of Congo (DRC), and South Africa (imported case) between 1994 and 1996. As doctors and scientists rushed in to contain the outbreaks, they were also able to collect viral samples, and trap animals and insects in the area, searching for a reservoir for the virus. In this decade, there have been almost yearly outbreaks of Ebola and/or the closely related Marburg virus in Africa, resulting in the discovery of both Ebola and Marburg infection in species of fruit bats–suggesting these animals may be a reservoir species for filoviruses (though more work remains to be done to confirm this).

As I blogged about previously, prior work has suggested that the most deadly Ebola subtype, known as Ebola-Zaire (EBO-Z) after its initial site of isolation, has been spreading steadily eastward across the central African continent. This was tracked by examining isolates of the virus obtained during human epidemics, which introduces a bias into the sample. However, viral isolates from other sources have been quite difficult to obtain, despite many years of searching. A new paper examines viral isolates collected from dead gorillas and reconstructs their phylogeny in an effort to fill in some of these gaps; more after the jump.
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