Population-based surveillance for MRSA

NHANES is an abbreviation that’s quite familiar to epidemiologists of all stripes: the National Health and Nutrition Examination Survey. This survey dates back to 1956 with the passage of the National Health Survey Act, providing legislative authorization for “a continuing survey to provide current statistical data on the amount, distribution, and effects of illness and disability in the United States.” Generally, information from these surveys has been used to look at the effect of nutrition, particularly micronutrients, on the health status of the population, or subgroups within the population. However, survey data and biological samples obtained from those enrolled in these studies can be used for other purposes as well—and one recent study took advantage of this. A new publication by Kuehnert et al. uses NHANES samples to examine colonization with Staphylococcus aureus. As with many pathogens, a significantly greater number of us are asymptomatic carriers of this bacterium than are sickened by the pathogen. Additionally, strains of S. aureus that is resistant to the antibiotic methicillin (methicillin-resistant S. aureus, MRSA) appear to be increasing in prevalence in the community. I say, “appear to be,” because no good, population-based study had been carried out to date. This new study begins to fill that void.

Samples from 9,622 people enrolled in the NHANES study in 2001-2 were examined for S. aureus colonization; almost a third (32.4%) were found to be positive. Extrapolating to the U.S. population, that means that almost 90 million people are colonized with this pathogen. Prevalence was found to be highest in the 6-11 year age group, and males were slightly more likely to be colonized than females.

75 of the S. aureus-colonized individuals were carrying MRSA–.8% of the population, or about 2.3 million Americans. In this analysis, MRSA was found more frequently in older age groups, and in females. However, when community-acquired MRSA (in contrast to nosocomially–or hospital-acquired–isolates) were analyzed separately, the groups most at risk again were young children and African-Americans. As previous studies have shown that those who are colonized are at a higher risk of subsequent MRSA disease, this puts a significant amount of our population–and particularly, our children–at risk of developing serious disease due to this bacterium, which is extremely difficult to treat.

Additionally, MRSA disease in individuals who have no nosocomial exposure has increased in the past several years. Since the data from this study comes from samples taken in 2001-2, these results can be compared to more recent data. For example, other studies conducted at various sites in 2001 found MRSA prevalence rates of .6-2.8%. However, by 2004, a study of 500 healthy children using identical methods found colonization rates of 9.2%, an increase of greater than 10-fold in that community. Likewise, a 2004 study of youths in San Francisco found a MRSA colonization rate of 6.2%, and a Texas study earlier this year reported a 22% MRSA colonization rate. Certainly with these numbers, the increasing find of community-acquired MRSA becomes much less surprising. The bad news is, we don’t currently have a way to keep this from increasing even further, and there are few options in the pipeline as far as treating MRSA. A vaccine is in the works, but clinical trials–for both vaccines and new drugs–take time and money. Meanwhile, thousands of people worldwide are dying from this pathogen each year. As usual, the best prevention is simply to wash your hands and generally practice good hygiene–something to keep in mind while you gather with your loved ones during this holiday season.

Cheers, and have a good one–I’ll be out for a few days with the kiddos and extended family myself.

Kitzmiller decision–required reading

kay, after going through the whole Kitzmiller decision last night, and damn, it’s good. Really, incredibly good. This should be required reading. Jones’ disgust at the whole thing comes through loud and clear. On page 29:

Although proponents of the IDM (Intelligent Design movement) occasionally suggest that the designer could be a space alien or a time-traveling cell biologist, no serious alternative to God as the designer has been proposed by members of the IDM, including Defendant’s expert witnesses.

He discussed this at length, clearly connecting the dots between the Discovery Institute, the Wedge Document, Pandas and People, right up to the Thomas More law center and the Dover school board. On page 31,

A “hypothetical reasonable observer,” adult or child, who is “aware of the history and context of the community and forum” is also presumed to know that ID is a form of creationism…The evidence at trial demonstrates that ID is nothing less than the progeny of creationism. What is likely the strongest evidence supporting the finding of ID’s creationist nature is the history and historical pedigree of the book to which students in Dover’s ninth grade biology class are referred, Pandas. Pandas is published by an organization called FTE, as noted, whose articles of incorporation and filings with the Internal Revenue Service describe it as a religious, Christian organization. Pandas was written by Dean Kenyon and Percival Davis, both acknowledged creationists, and Nancy Pearcey, a Young Earth Creationist, contributed to the work.

As Plaintiffs meticulously and effectively presented to the Court, Pandas went through many drafts, several of which were completed prior to and some after the Supreme Court’s decision in Edwards, which held that the Constitution forbids teaching creationism as science. By comparing the pre and post Edwards drafts of Pandas, three astonishing points emerge: (1) the definition for creation science in early drafts is identical to the definition of ID; (2) cognates of the word creation, which appeared approximately 150 times were deliberately and systematically replaced with the phrase ID; (3) the changes occurred shortly after the Supreme Court held that creation science is religious and cannot be taught in public school science classes in Edwards.

The Pandas book was definitely a slam-dunk, though many other factors clearly contributed as well: the history of the decision by the Dover board to have their teachers announce the disclaimer, and the adoption of the Pandas book as an “alternative” text (and the lies that were told about it during the trial); the Wedge document; Behe’s arrogant testimony (dissected further at Pharyngula); and the overwhelming view from the community that ID was indeed religious, as measured by opinion letters in the local newspapers. The latter is something that could be very important in any future trials of this nature: even if the proponents are careful to say that the designer in ID can be “a time-travelling cell bioloist” or whatever, the community is going to be more vocal in their belief that ID is a religious idea, and the designer is God.

This, truly, has given those of us who’ve been fighting ID a “merry Kitzmas.”

Edited to add: Ed and Burt’s Skeptic article about the trial has been released here with some more “behind the scenes” material. Check it out. Additionally, for a one-stop-shop of links to discussion of the trial and the decision, check out The Questionable Authority.


Plaintiffs Prevail

The much-awaited decision in the Kitzmiller et al. v. Dover Area School District is now available.

The 139 page document finds for the plaintiffs.

Judge Jones finds that “intelligent design” is not science. The DASD ID policy violates both purpose and effect prongs of the Lemon test, and also violates the Pennsylvania constitution.

Much more here, here, and here, and I’m sure more will follow. (Update: Ed has a “thank you” list here, and Mike mentions others here. As someone who got to watch a bit behind the scenes, there was definitely an amazing amount of work that went into this case–and what I saw was only the tip of the iceberg. Kudos to everyone involved.)

Haven’t read the (139 page!) decision yet–perhaps my reading for tonight.

Update: Discovery Institute pans the ruling, calls Jones an “activist judge:” link. Funny that Jones was appointed by GW…

Six years ago today

…I was suffering the worst pain I’d ever experienced. I arrived at the hospital a bit before 1AM, and spent the next four hours or so walking around in agony. By 5AM, I decided I was ready for some of the good drugs, but the nurse informed me it was too late–time for the real fun to start. My daughter was born at 5:23AM, December 13, 1999–five long grumpy days after her due date. I was supposed to have a final exam that day.

My daughter wasn’t exactly, erm, scheduled–but no contraceptive is 100% effective. I’d just been accepted to grad school, married less than 6 months, and hello, baby on the way. Kids had always been in the long-term plan, and since where my husband and I grew up, 23 was practically ancient to have your first baby, we bought a crib, set up a nursery, and hunkered down to become parents. It occurred to me for all of a minute to postpone grad school, but I’ve always been up for a challenge, so never gave that option serious consideration. I admit, though, that it was unnerving to say the least to be sitting in class during the last trimester of my pregnancy, discussing every possible chromosomal and developmental abnormality that can happen during development, with outcomes ranging from mildly bad to, of course, fatal. *Not* recommended for the faint of heart.

Luckily, she had pretty good timing. A mid-December birth meant that I already had Christmas and New Year’s off, so I didn’t have to miss too much time in the lab. I took off exactly 4 weeks (though I made up the missed exam a week after she was born), then headed back to the lab. Since daycare was a huge financial burden on a grad student’s stipend, we got creative. My husband had a 7-to-4 job, so I worked around that, going in a lot of weekends and generally staying home one or two days during the “normal” work week to cut daycare costs. Again, I was fortunate: I’d already worked in the lab for almost a year prior as a technician, so even though I’d officially been a grad student for only a few months, I was already independent in the lab and didn’t need someone to watch over my shoulder–allowing me to be in there on a Sunday at 7AM or a Wednesday at 1AM and get my work done.

Being a parent and a graduate student ain’t easy. Obviously, the money sucks–at that time, my stipend was just over $13,000/year, and then they took out more every month for parking and health insurance. At my school, the health care also was pretty terrible: incredibly, though well-baby checkups were paid for, infant vaccinations weren’t even covered. To top things off, I had (make that *have*) pretty hefty student loan payments from undergrad. Nothing like using the ol’ charge card for diapers and groceries.

Anyway, since Baby #1 was the model of cherubic perfection (as of course, everyone thinks their own children are), and since my husband and I both have siblings who are close to us in age and we wanted that for our own children, we decided to confirm the fact that we were, indeed, insane. Baby #2 came along toward the other end of my PhD. (He was right on time, and no test that day–I was scheduled to give a journal club presentation. I’d already passed the file along to someone else, “just in case.”)

Postdoc ensues, then I get to move up in the world as an assistant professor. Though family issues have always been a worry, now is when it really starts to kick in. (See, for example, this discussion, or this horror story). Again, I’m lucky on one level–I’m not planning on having any more children, so I don’t have to worry about pregnancy, or maternity leave, or any of that jazz. I don’t need to stress and tear my hair out trying to find the “right time” to start a family, since I already finished mine during probably the least-recommended stage of my career. My daughter is in kindergarten and my son goes to preschool, so our childcare expenses aren’t quite as horrible as they once were. My husband now has his own business, so if I need him to watch the kids for some reason, he’s flexible. But like many women in all different kinds of careers, I still feel pulled in a million different directions, and still worry about how taking time out for my kids will impact my career, and how spending so much time at my job will affect my children.

I’m all too familiar with the arguments on both sides of the “academics and children” fence. “Overall, academics have it good.” We’re “spoiled, whiny complainers;” we “want it all and don’t want to sacrifice job or family;” our “ambitions are too high, we should lower them” (especially true for women who want a satisfying family life); “hey, the system as it works now gave us quantum mechanics and the Internet, so why fix what ain’t broken?” On the other side, “academia loses a lot of good teachers and researchers when it comes down to a choice between family and career”–and besides, “how would we con those naive, innocent grad students into aspiring to stay in academia without some kind of move forward on family issues?”

In the discussion referenced above, physicist Ann Nelson left this comment (which sums up my feelings pretty well, and having an authority say it is even better):

The problem is that most people ASSUME that a woman cannot be a good mother and a good scientist. So at work we always feel we have to prove ourselves and do extra so people don’t say “see, she can’t be serious about science because she is a mother”. Then women who do need to take some leave or some time to breastfeed or need to leave work to pick up a sick kid worry that this is going to lead their colleagues to assume they have lost their committment to science. The other side of the pressure and stress is caused by the very large number of people who assume that only a SAHM [stay-at-home mom] can be a good mother, and a career oriented woman must be some kind of neglectful mother who is having her kids raised by strangers.

So, yeah, there’s this too–guilt from all sides. You’re never good enough as a scientist because you have a life away from the lab. You’re never good enough as a mother because you have a life away from the kids. Is this just our paranoia, or does it really represent what people think? Do people really *say* this to us? Rarely–but it does happen. More often, I’ll read it somewhere: a comment from a scientist about other scientists with families, and how their priorities aren’t in line (or, one of the more overtly insulting lines I mentioned above). Or I’ll see or hear a similar comment from a SAHM who is sure I’m screwing up my kids’ psyches by having a demanding career.

Anyway, I worry, and I stress, and at the same time, I make the most of it. By all reports, my kids are doing great in school, both academically (well, as academic as kindergarten and preschool get) and socially. I’ve been here for almost a year now, am currently working on getting some more manuscripts submitted, and think I’ve had a pretty productive year. Things aren’t going quite as swimingly in the lab, but I’ll be starting at least 2 new projects after the new year, which will (hopefully) mean more papers and more grants, potentially by this coming summer. Next fall will bring more teaching duties, but it’s a course I’ve taught before, so at least I’m not quite starting from scratch. In between, there will be birthday parties, and trips to the park and the lake, and Disney movies, and ice skating. And lots of creature-catching: we currently have about 5 wolf spiders in various jars around the house, and a small frog she caught in the creek out back in late fall as “pets.” And yes, it will probably mean a few weekend mornings spent coloring in Mom’s office while I finish up some work. If they need therapy as adults because of this horrible treatment, maybe I’ll chip in for half.

Happy birthday, baby girl. I hope that 20 years down the line, the idea that you have to make a choice between your dreams and your family will seem a backwards and archaic notion, and that you go as far as you want along whatever path you choose. I may have to come with a journal article and highlighter in hand, but I’ll be there, cheering you on.

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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Are fruit bats a reservoir for Ebola?

As I’ve mentioned before, Ebola is a virus near and dear to my heart. (Figuratively, not literally. I’m not quite that enamored of it). In that previous post, I mentioned that we didn’t know the reservoir of Ebola in nature. It certainly isn’t for lack of trying that it wasn’t determined previously. The first field studies took place shortly after the initial 1976 outbreaks in the Democratic Republic of Congo (DRC) and Sudan. In the former, 818 bedbugs, 1500 mosquitoes, 10 domestic pigs, one cow, seven bats, 123 rodents, eight squirrels, six Cercopithecus monkeys, and three small antelopes were sampled–all negative when viral isolation was attempted. In Sudan, almost 500 vertebrates were similarly tested–zilch. Similar results in 1977 and 1979 in the DRC. Following that outbreak, Ebola did not re-surface for a decade and a half, popping up again in a large 1995 outbreak in Kikwit, DRC. A total of 2814 vertebrates and a whopping 27,843 arthropods were captured during respective periods of 3 and 6 months after the end of the outbreak. Viral isolation was attempted from both categories of animals, and vertebrates were also tested for Ebola-Zaire-specific IgG. No positive IgG reactions were obtained, and no viruses were isolated on Vero cells. The vertebrates included 1759 rodents, 539 bats, 114 insectivores, 184 birds, and 127 reptiles and amphibians. The arthropods included 15,118 mosquitoes, 124 blood-sucking flies, 6538 bedbugs, 144 fleas, 103 lice, and 5816 ticks.
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