Not the Batman kind–the influenza kind.

I received a questionnaire yesterday from ABC news. Apparently, they’re doing a story on pandemic influenza preparation. Included were questions like, “What would you recommend to those individuals who are trying to obtain antiviral medications for their own personal preparedness? When should they start taking them?” and “What would you recommend to individuals who are trying to obtain face masks for their own personal preparedness? When should they start wearing them?”, as well as questions about food and water stockpiling and going to work/school. (More below…)
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“Flesh eating” bacteria strikes Boulder

Necrotizing fasciitis (the so-called “flesh-eating disease”) is a rare manifestation of infection with the group A streptococcus (Streptococcus pyogenes, though occasionally other bacteria cause it as well). Apparently, it’s been a banner year for the infection in Boulder, Colorado. The Daily Camera (registration required) has the story:

Sixteen months after University of Colorado physicist Eric Cornell lost his left arm and shoulder to a rare, invasive form of strep A, at least three more otherwise healthy Boulder residents have been stricken by the same disease in the past four months.

Two who live within one-half mile of each other developed necrotizing fasciitis, otherwise known as flesh-eating bacteria, and had to have multiple surgeries to remove infected tissue. A third developed an infection in the blood and brain and died within 48 hours after first complaining of an ear infection.
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Why Nigeria for first African H5N1 outbreak?

This question was discussed yesterday in the comments to this post. An article in yesterday’s New Scientist offers some ideas:

But New Scientist can reveal that the location of Africa’s first reported outbreak should not come as a surprise. The region affected is right beside a major wintering ground for two relatively common species of duck. Those ducks shared breeding grounds in Siberia last summer with birds that winter in Turkey and around the Black Sea, where the virus also appeared recently.

Furthermore, Kano is near the Hadejia-Nguru inland river delta, which is a major wintering location for Northern pintail and garganey ducks. These species summer in breeding grounds across Siberia, where the Qinghai strain of H5N1 infected poultry and wild birds in summer 2005. They then winter in Turkey, around the Black Sea, and in West Africa. The Qinghai strain has already broken out in Turkey and around the Black Sea, apparently carried by migrants.

The authoritative 1996 Atlas of Anatidae [ducks, geese and swans] Populations of Africa and Western Europe says the Northern pintail wintering in the Black Sea and Mediterranean basins “are lumped with those wintering in West Africa as a single large population”. On average, 18,000 pintails winter each year at Hadejia-Nguru. Similar numbers of garganey ducks follow the same migration and 500,000 of each species winter at nearby Lake Chad.

Some of the Northern pintail wintering now in Britain and along Europe’s North Sea and Atlantic coasts also spent last summer on the same breeding grounds as the pintail that subsequently flew to the Black Sea, Turkey and West Africa.

So, there’s one explanation. I’m not enough of a bird person to know if it’s a good one or not, however.


Aflatoxin found in pet food

I’ve been meaning to write something up about this for awhile, but keep forgetting. Anyhoo, because my own dog is currently ill and it’s stressing me out watching her (not due to this, thankfully), I thought I’d do my own little part to get the word out to any dog owners who may not have heard of this recall.

Diamond Pet Food Recalled Due to Aflatoxin

Diamond Pet Food has discovered aflatoxin in a product manufactured at our facility in Gaston, South Carolina. Aflatoxin is a naturally occurring toxic chemical by-product from the growth of the fungus Aspergillus flavus,, on corn and other crops.

Out of an abundance of caution, we have notified our distributors and recommended they hold the sale of all Diamond Pet Food products formulated with corn that were produced out of our Gaston facility (see complete list below). Please note that products manufactured at our facilities in Meta, Missouri and Lathrop, California are not affected. The Gaston facility date codes are unique from other Diamond facility codes in that either the eleventh or twelfth character in the date code will be a capital “G” (in reference to Gaston). The range of date codes being reviewed are “Best By 01-March-07″ through Best By ” 11-June-07″. Diamond’s quantitative analysis records substantiate that Diamond’s corn shipments were definitively clear of aflatoxin after December 10. As such, “Best By 11-June-07” date codes or later are not affected by this notice.

States serviced by our Gaston facility include Alabama, Connecticut, Delaware, Florida, Georgia, Kentucky (eastern), Maine, Maryland, Massachusetts, Mississippi, New Hampshire, New Jersey, New York, North Carolina, Ohio, Pennsylvania, Rhode Island, South Carolina, Tennessee, West Virginia, Vermont, and Virginia.

We are rapidly analyzing retained samples of all products produced in Gaston so we can isolate specific lot numbers impacted and provide this information to our distributors, retailers and customers as quickly as possible.

Meanwhile, if your pet is showing any symptoms of illness, including sluggishness or lethargy combined with a reluctance to eat, yellowish tint to the eyes and/or gums, and severe or bloody diarrhea, please consult your veterinarian immediately.

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Emergence of epidemic Clostridium difficile

Clostridium difficile has joined MRSA, SARS, avian influenza, and West Nile as a hot new emerging disease. This bacterium, a cousin to Clostridium tetani-the causative agent of tetanus–and Clostridium botulinum–the botulism bacterium–is a spore-forming anaerobe. Carried by about 3 percent of healthy adults, the bacterium is generally present as a metabolically inactive spore. The bacterium typically causes problems in the nosocomial (hospital) environment, where up to 40 percent of hospital patients may be colonized. Clinical disease generally presents as watery diarrhea and cramps, and is the most frequent infectious cause of nosocomial diarrhea, resulting in about 3 million cases per year. Mortality is generally low (less than 3 percent). Though not commonly fatal, these infections have a high monetary cost: each infection results in ~$3600 in excess health care costs, for a total of over $1 billion in the United States alone every year.
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New vaccine recommendations coming

Doctors recommend hepatitis shot for kids

Hepatitis A is a virus that causes (obviously) hepatitis, as well as jaundice, fatigue, nausea, fever, loss of appetite, and diarrhea. It’s often spread fecal-orally; that is, you put something in your mouth that has fecal contamination. (Just makes you want to run to the bathroom and brush your teeth, doesn’t it?) It also can be spread via sexual contact and shared needles (or other contact with blood or body fluids). It’s estimated that there are ~40,000 acute cases of Hep A per year, with many of them going undiagnosed. It’s one of those diseases that you don’t hear about until there’s an outbreak (like this one), but it causes a significant amount of morbidity in the U.S. every year. Hence, the new recommendations:

The Advisory Committee on Immunization Practices, which helps set federal vaccination guidelines, voted unanimously to recommend that a two-dose vaccination be given young children. The panel’s recommendations are routinely adopted by federal health officials and are influential to doctors.

Expanding the vaccination recommendation to all the states could prevent 100,000 cases and 20 deaths in the lifetimes of children vaccinated in one year. The direct costs of the vaccine program, currently at $22 million, would increase to $134 million.

Also new is the recommendation to add pertussis to the tetanus-diptheria booster shot for adults. Bordatella pertussis is the cause of whooping cough, a rare disease now but one that caused a lot of misery (and a lot of mortality) in the pre-vaccine years. Children are still vaccinated against it, but there are 2 problems: 1) insufficient vaccine coverage, as parents refuse to have their children vaccinated due to religious objections or fear of side effects, and 2) infection of infants before the vaccination has elicited immunity. The bad thing about pertussis is that the vaccine wears off after 5 years or so, meaning that adults have little or no immunity. This isn’t a big deal for we “grown-ups,” as pertussis doesn’t cause such serious disease in adults. What it’s a problem for are adults who are around incompletely vaccinated infants or children: if the adult is a carrier, they can pass the bacterium to a child, causing illness in the recipient. And there has been a resurgence of pertussis in recent years:

Since pregnant women are one group that will be in contact with both unvaccinated infants and waaaay too much fecal material, they’re an ideal target for both of these vaccines. I’ve already passed along the recommendations to my expectant sister so that she can discuss it with her M.D.

What the hell is going on with Tularemia? or, a Rant about public health problems

It’s situations like this that really irk me.

I mentioned the tularemia detection in DC here almost 2 weeks ago, already annoyed that there hadn’t been more information about it. There has been some discussion on the ProMed list, but it’s hardly been a blip in the mainstream media. Yesterday, there was an article in Salon further discussing it.

The background:

On Sept. 24, 2005, tens of thousands of protesters marched past the White House and flooded the National Mall near 17th Street and Constitution Avenue. They had arrived from all over the country for a day of speeches and concerts to protest the war in Iraq. It may have been the biggest antiwar rally since Vietnam. A light rain fell early in the day and most of the afternoon was cool and overcast.

Unknown to the crowd, biological-weapons sensors, scattered for miles across Washington by the Department of Homeland Security, were quietly doing their work. The machines are designed to detect killer pathogens. Sometime between 10 a.m. on Sept. 24 and 10 a.m. on Sept. 25, six of those machines sucked in trace amounts of deadly bacteria called Francisella tularensis. The government fears it is one of six biological weapons most likely to be used against the United States.

Tularemia is a naturally-occurring, albeit rare, disease. The bacterium, Francisella tularensis, can infect a wide variety of animals, and can be spread in a number of ways: via ticks, contact with infected animals (this used to be a disease that was fairly common in hunters and trappers, and is nicknamed “rabbit fever”), drinking contaminated water, and airborne spread if the pathogen is aerosolized in some manner. (When I was first taking infectious disease epidemiology, it was mentioned that at least one pulmonary case was due to a rabbit puree which had been created when an infected rabbit was run over by a lawn mower. Similar cases in landscapers have been documented in Martha’s Vineyard). It also is a potential biowarfare agent, due to the fact that it can spread fairly easily via aerosol, and that the infectious dose is incredibly low: as few as 10 inhaled organisms can cause disease.

So, when this bug was detected in 6 sensors in our nation’s capital, at the same time as a large march in the area, wouldn’t you think that would be some headline news? Hell, at least the second section?

Yet it’s barely a blip on the nation’s radar. Even many infectious disease folks I’ve spoken to haven’t heard of it, and certainly the public at large is largely ignorant that anything happened. And that would be fine–I understand very well the conflicting desire to inform people about what was detected by the sensors, and at the same time, to educate them about how the tests work, the false positive rate, and other issues so that no one freaks out about something that may turn out to be a false alarm. But some of the revelations in this article are stunning. For example:

The DHS scrambled for three days to confirm just what may have been in the air that day. On Sept. 27, it turned for help to the Centers for Disease Control and Prevention. The CDC did its own tests, and on Sept. 30 — six days after the deadly pathogens set off the sensors and well into the incubation period for tularemia — alerted public health officials across the country to be on the lookout for tularemia, the deadly disease caused by F. tularensis.

“It is alarming that health officials … were only notified six days after the bacteria was first detected,” House Government Reform chairman Tom Davis, R-Va., wrote in an Oct. 3 letter to Homeland Security Secretary Michael Chertoff. “Have DHS and CDC analysts been able to determine if the pathogen detected was naturally occurring or the result of a terrorist attack?”

(Emphasis mine) 6 days for notification of health officials? These are the very people who should be warned ASAP. They should, theoretically, have some training in bioterrorist events, and know that in the early stages, it’s pretty unlikely that a positive sensor means a bioterrorist attack, so the “public fear” issues that may keep some reporters from holding a story back shouldn’t apply there. It should have been especially critical to notify them, as people from all over the country had flocked to the peace rally right where all those detectors went off. Luckily, tularemia isn’t spread person-to-person, but the local health departments should have at least been put on alert to keep an eye out for potential cases.

Moving on,

“It is not unreasonable that this is a natural occurrence,” says Von Roebuck, spokesman for the CDC. “There are still no cases of tularemia.”

I’ll discuss his “no cases” assertion a bit later, but regarding the naural occurrence scenario, sure, it’s not totally unreasonable. I’ve seen estimates from 150,000 to 300,000 people involved in the September rally; lots of people around, kicking up dust. Would it be enough, though, and is tularemia even present in D.C.? Ideally, when any environmental sensors of this type are installed, the background levels of contamination should be determined first, so you know how much “noise” there is in the environment. I don’t know if this was done with tularemia in D.C. (though I have to say, I doubt it). Had it been, we could already have data on the presence of naturally-occurring tularemia there. For instance, there certainly are a lot of squirrels in that area, and tularemia may be endemic in them. Testing of the rodent population there could further that hypothesis. One could also look at the molecular epidemiology of the pathogen population to see if the strain(s?) of tularemia isolated from the sensors matched up with ones found naturally in D.C. I’d assume some of this is being done now–at least, I hope it is.

BUT–according to the Salon article, those marchers would have to have been kickin’ up some major dust:

There was another troubling thing. One of the sensors that went off was located at the Lincoln Memorial on the far western end of the Mall. Another was located near Judiciary Square, roughly two miles to the east and two blocks north of the Mall. A third was at the Army’s Fort McNair, more than two miles from the Lincoln Memorial down the Potomac River past the Mall, on the point of land where the Washington Channel and Anacostia River meet. The locations of the other three sensors have not been disclosed.

It seems pretty unlikely that the soil could have been that contaminated, yet they’d never had a sensor pick this up before.

As far as the earlier assertion that there haven’t been any cases, well, maybe there have, maybe not. Tularemia is also one of those pathogens that causes a “flu-like illness:” fever, chills, headache, muscle aches, cough, and weakness, with serious cases progressing to pneumonia and respiratory failure. It’s very treatable with antibiotics, so it’s certainly possible that many people have simply gone to their physician and were treated without ever having the causative pathogen isolated. The Salon article found several people who reported symptoms similar to those caused by F. tularensis; some went to the doctor, at least one did not. Had more been made of this in the national media, perhaps more people would have checked in with their physicians, and we could at least have samples to test for the bacterium. As it stands now, we don’t know whether people were really infected, or not; and if they were, whether it was due to an actual terrorist event, or not.

Feeling safe yet?

In September, I wrote a post over on Panda’s thumb discussing the 2001 anthrax attacks; y’know, the ones that were very obviously bioterrorism, yet we still have no clue about. And today on Effect Measure, Revere discusses administration policies (specifically, funding cuts) and their effects on public health and beyond:

The cuts are independent of the concern for influenza. They are a consequence of the wrecking-ball policies of the Bush Administration and the Republican-controlled congress (and shame to the democrats who helped). You don’t stop a wrecking-ball in mid-swing. It has too much inertia and will continue to destroy critical infrastructure even as bandaids like supplementary avian flu funding try to cover the worst of the damage.

It’s not just public health. It’s dams, bridges, levees, the shredded safety-net for our most vulnerable neighbors. While pursuing military adventures abroad and obsessed with terrorists at home, the BushCo’s left us defenseless and dangerously vulnerable in our own homes, workplaces and communities.

(Emphasis mine). And that’s exactly the problem. We keep hearing over and over how we’re “fighting the terrorists” and “taking the war to them,” yada yada yada, yet we may have just been attacked in our own national capital with a real WMD, and no one’s paying attention. All the attention to avian flu has been great, but the Powers That Be really need to wake up and realize that if they really want to do something to increase our safety, they should be investing more money here at home in better public health programs that will benefit everyone, instead of throwing some money here and there at different hot topics and hoping that will make them go away–it’s crystal clear that’s simply not working.

Dobzhansky and anthrax

The Washington Post today reminds us that there has been little progress in uncovering the source of the 2001 anthrax attacks. [1]

First, a disclaimer. I’m not an “evolutionary biologist,” per se. I have what is I swear the longest job title ever–molecular infectious disease epidemiologist. As such, I often get asked, “what’s the relevance of evolution to your work?” Or, I’ll read editorials such as Dr. Skell’s recently in The Scientist [2] questioning the use of evolutionary theory in experimental biology, and be disheartened. Yet the method of investigating the anthrax attacks shows once again just how relevant evolutionary theory is to all areas of biology, and how Dobzhansky’s famous “Nothing makes sense…” comment once again ring true.

There are several clues regarding the 2001 attack (for those unfamiliar with the story, the background can be found here) [3]. Some are in the packaging of the material: the writing on the envelope, the location of the postmark, the mailbox where the letters were dropped. Others are in the processing of the anthrax: the spores were finely milled, so as to be more easily aerosolized. Finally, there are clues in the bacteria themselves: in their genetic makeup. Early on, they looked at the molecular profiles of the anthrax and compared them to known strains, zeroing in on the Ames anthrax strain.

This is a good thing, because the Ames strain is fairly rare in nature–making it more likely that the anthrax was obtained from a laboratory. The problem with anthrax, however, is that as a species, it is very homogeneous: there isn’t a lot of variation in the DNA sequence. Fingerprinting techniques like pulse field gel electrophoresis (PFGE), which uses restriction enzymes to cut the bacterial chromosome into smaller pieces to be run out on agarose gels, work well for pathogens like E. coli and Staphylococcus aureus, but isn’t nearly as useful in anthrax due to the low level of sequence diversity. This makes it necessary to use more sensitive techniques to identify the bacterium, bringing us back to the characterization of the 2001 bioterrorist strain as the Ames anthrax strain.

What is the “Ames strain,” exactly? In a 2001 Science article [4], it was noted that

Over the past 2 decades, the U.S. Army Medical Research Institute of Infectious Diseases [USAMRIID] in Fort Detrick, Maryland, sent the Ames strain to several research labs. And as it was passed around and grown in different labs, it may well have accumulated minute new changes.

Researcher Martin Hugh-Jones noted, “The Ames strain can be many different things. A very detailed fingerprint could reveal very very minor variations.”

Therefore, it’s the accumulation of these mutations–from a common ancestor, the original “Ames strain” (sound familiar?)–that may allow for a more specific determination of the origin of the 2001 strain, shedding light on the most notable biocrime in recent history. I’ve not seen a published comparison of the whole genome sequences of the various Ames strains, but that seems like the logical way to proceed in this (apparently stalled) investigation–go right back to that “useless” evolutionary biology to save the day.


[1] Lengel, A. “Little progress in FBI probe of anthrax attacks.” Washington Post. September 16, 2005.
[2] Skell, PS. 2005. “Why do we invoke Darwin? Evolutionary theory contributes little to experimental biology.” The Scientist. 19:10.
[4] Enserink, M. 2001. “Taking anthrax’s genetic fingerprints.” Science: 294; 1810-2.