microbiology
mikethemadbiologist | January 2, 2007So Michael Fumento has issued a challenge to put 'odds' on avian influenza, thinking that somehow I've stated that an avian influenza pandemic is likely (he's also accused me, a scientist, of being "anti-scientist" and "alarmist"). Well, I'm not putting odds down because I've never said that a pandemic is likely. Then again, one should hardly be surprised when a professional conservative completely distorts what one says.
In fact, in the post, I wrote:
We can argue about public health priorities (avian flu isn't my top priority personally).
One would think that was clear, but I made the…
sporte | January 2, 2007After reading Kevin C.'s question in the comments on my last antibiotic post, I decided to look into this question a bit further.
As far as I can tell, most of the commercially producted antibiotics are made by bacteria, fungi, and a bit chemistry (more on that in a moment). It appears, however, that compounds with antimicrobial properties are made by just about everything. Just to make things complicated, these molecules are sometimes called "antibiotics" in the literature and sometimes they're not.
Many of the molecules with antimicrobial activity are short peptides- chains of amino…
mikethemadbiologist | January 1, 2007From the archives, here's another post about influenza.
...you knew that starting in late September or early October there would be a series of bioterrorist attacks, and that these attacks would kill anywhere from 30,000 - 50,000 U.S. citizens. Now imagine that you could produce a vaccine that would be, at worst partially effective, and at best, completely effective, particularly if enough of the U.S. population were vaccinated. Imagine that, with enough vaccination, thousands of lives could be saved. A competent government, one that could do a heckuva job, would do something, wouldn't it…
mikethemadbiologist | December 31, 2006I've been called out by Michael Fumento regarding a post about avian influenza. While I'm putting that together, I thought it would be a good opportunity to revisit some previous posts about influenza. From the old site:
A think tank in Australia released a report claiming that an influenza pandemic might kill over 140 million people. So, after spending most of my professional career examining the evolution of infectious disease, I think...I don't have any idea if a pandemic influenza strain will evolve. Ultimately, we're trying to anticipate a unique historically contingent event:…
sporte | December 30, 2006This is multipart series on antibiotic resistance in bacteria.
Check out the previous bits:
1. A primer on antibiotic resistance
2. Natural vs. synthetic drugs
Eventually, we'll reach the ways in which bacteria develop antibiotic resistance, but before we get there, we'll spend a little more time on antibiotics themselves.
What have we learned so far?
1. Antibiotics are natural products, made by bacteria and some fungi.
We have also learned about the difference between antibiotics and synthetic drugs. There isn't always a clear distinction since chemical groups can be added to…
mikethemadbiologist | December 27, 2006Thankfully for the readers, most of the scientific literature I read doesn't make it into this blog. But one paper about a comparative drug trial had some very interesting results. In short, obesity and smoking are significant risk factors for post-operative infections.
The article, published in the NE Journal of Medicine, is a comparative study of which is the better antibiotic use to use after colorectal surgery to prevent infections: etrapenem or cefotetan. While cefotetan is typically used, etrapenem was was associated with significantly fewer post-operative complications.…
mikethemadbiologist | December 26, 2006From the archives, I'm reposting this article about MRSA and VRSA. I've made some changes because the science and medical practice have changed.
The Chicago Tribune reports that three children died from toxic shock syndrome caused by methicillin resistant Staphylococcus aureus ("MRSA"). Toxic shock syndrome is not typically associated with MRSA. What's worse is that these infections were "community-acquired" (CA-MRSA) In other words, the kids were not infected in the hospital-many staph infections are hospital acquired due to puncturing the skin barrier (e.g., catheters, IVs, surgery).…
sporte | December 26, 2006In case you missed it, the December edition of Animalcules is posted at Aetiology. Look for lots of enjoyable reading about our invisible friends.
mikethemadbiologist | December 24, 2006...so no blogging. Instead, I'll leave you with a "make sexy time" photo (to steal Borat's phrase):
It's E. coli having sex. Well, actually it's conjugation. Many bacteria have plasmids which are 'mini-chromosomes' (antibiotic resistance genes are often found on plasmids). The bacteria are able to build protein tubes ("pili") and send copies of plasmids to another cell.
mikethemadbiologist | December 23, 2006At a recent conference (pdf), Dr. Rebecca Roberts described how medical residents and doctors treat urinary tract infections. But first, a bit about 'empirical therapy.'
When a patient is sick it can take anywhere from 24-72 hours at a hospital with good facilities to identify what organism is causing the disease and which antibiotics will be effective against it. Empirical therapy uses the patterns of resistance (and infections) of previous cases at the hospital in conjunction with other guidelines to choose the most effective antibiotic therapy. Think of it as a highly educated guess--…
mikethemadbiologist | December 22, 2006At a recent conference I attended (pdf file), one speaker (Dominique Monnet) presented a very interesting observation about the relationship between the number of different antibiotics available and the amount of antibiotics prescribed.
Quite simply, as the number of potential competiting drugs increases, the amount of drugs prescribed increases:
(from here; the y-axis is the number of daily doses per 1000 residents)
There are at least two reasons for this pattern:
1) Advertising aimed at doctors and hospitals is more likely to increase use simply because doctors will be influenced to use…
sporte | December 22, 2006Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants?
Two reports in Nature (1, 2) suggest that bacterial populations differ between people who are obese and people who not, and that the bacterial inhabitants of their guts, may be partly to blame.
In one study, the authors studied the bacterial populations of their volunteers' intestines by compiling a data set of 18,348 DNA sequences for bacterial 16S ribosomal RNA by sampling feces. Wow! That's a lot of ... well, I won't say it, but you know what I mean. In…
mikethemadbiologist | December 20, 2006At a recent conference (pdf), I heard Dr. Rebecca Roberts describe the economic cost of antibiotic resistant infections at Cook County's Stroger Hospital. In a nutshell, it's terrifying.
The average cost per patient at that hospital is $10,000. The cost of treating an antibiotic resistant infection excluding acute respiratory infections ('ARI')--this does not include the average cost of antibiotic sensitive infections--is $1,934. That is, of the $10,000 average cost, $1,934 goes to 'subsidize' the cost of antibiotic resistant infections. The $1,934 figure is the low estimate: the average…
mikethemadbiologist | December 19, 2006...or at least, I was mentioned in Cell. Currently, we have very few new antibiotics in the pipeline, particularly for Gram-negative bacteria such as Acinetobacter. One of the things I'm involved with is a project to develop a not-for-profit screening library to find new antibiotics. From Cell:
Resistance of microbial pathogens to an increasing number of antibiotics is a serious problem. In the US alone, 90,000 people die every year from infections acquired while in the hospital. According to the Infectious Disease Society of America (IDSA), 70% of these deaths have been attributed to…
mikethemadbiologist | December 17, 2006Well, we do it for narcotics. From Yahoo News:
International experts debated whether antibiotics merit a separate regulatory drug category at a World Congress held on December 11 and 12 at the Hyatt Regency Boston Hotel. "We proposed this drastic action because antibiotic resistance is undermining infectious disease treatment worldwide and many large pharmaceutical companies are leaving the antibiotic field," explains Stuart B. Levy, MD, a Tufts Medical School professor and president of APUA, the global public health organization convening the meeting. Pharmaceutical companies spend an…
mikethemadbiologist | December 16, 2006In the past week, over 400 students and teachers in the Boston area have contracted norovirus, which causes nausea, vomitting and diarrhea:
"In close settings like a school or a nursing home or a family, the failure to adequately follow good hygiene will manifest itself with spread of this type of disease," said Dr. Bela Matyas of the Massachusetts Department of Public Health.
At Simmons, the outbreak traveled swiftly, although it was not concentrated in any single location, said Dr. Kay Petersen , medical director of the college's health center. To stem the spread, e-mails were sent to…
mikethemadbiologist | December 15, 2006I was recently at a conference (pdf file) where one speaker (Dr. Thomas O'Brien) suggested 'VRSA hospital insurance' to prevent the spread of vancomycin resistant Staphylococcus aureus outbreaks ('VRSA'). Before I get into the plan, let's talk about VRSA.
VRSA are staphylococci which are not only resistant to vancomycin, which is one of the last effective drugs against methicillin resistant Staphylococcus aureus ('MRSA'), but are also resistant to most (or usually) all other available antibiotics. While tigecycline can be used to treat some infections (skin and abdomindal), it is not used…
mikethemadbiologist | December 10, 2006Biologist Esther Lederberg died recently--unfortunately, it wasn't very well covered (the NY Times was only a month late...). This is a real shame, since I don't think the history of molecular biology would have been the same without her.
While many people are familiar with, or at least have heard of her ex-husband, Joshua Lederberg, Esther Lederberg made seminal discoveries about the prophage Lambda. Lambda is a virus (or 'bacteriophage') that infects bacteria. Lambda can behave lytically--it injects its DNA into the bacterial cell, hijacks the cellular machinery to produce more virus,…
mikethemadbiologist | December 5, 2006In Las Vegas, the SEIU nurses were recently locked out during contract negotiations (they're back to work now). The nurses don't want pay increases or better benefits, but a lower patient-to-nurse ratio. Universal Health Services, the for-profit hospital chain, claims the nurses are trying to expand the union membership. The nurses claim that they simply want to improve patient care. Regardless of the motives involved, there is one indisputable fact: having fewer patients per nurse decreases the likelihood that a patient will become infected while in the hospital.
I've blogged about…
mikethemadbiologist | December 5, 2006I've posted before about the possible approval of cefquinome in agriculture, and why this is a stupid thing to even consider. So some colleagues and I got cranky and wrote a letter to the FDA.
Here's the letter:
Andrew C. von Eschenbach, M.D.
Acting Commissioner
U.S. Food and Drug Administration
5600 Fishers Lane,
Rockville MD 20857-000
Dear Acting Commissioner von Eschenbach,
We are writing to support the recommendation of the VMAC to reject and not approve the use of cefquinome, a fourth-generation cephalosporin antibiotic, for use in animal agriculture. One area that is critical in…