E. coli
mikethemadbiologist | March 8, 2010I'm conflicted about Nicholas Kristof's recent op-ed about antibiotic resistant organisms. On the one hand, Kristof is one of the only national columnists to raise this issue at all. On the other hand, I found his most recent column somewhat confusing--and I'm an expert in this area (I also think he's jumping to unfounded conclusions, but more about that later in the post). I think this is largely an effect similar to playing "telephone": information is being transferred multiple times from the primary source and finally conveyed by someone with no biological training. So what I'm going…
mikethemadbiologist | December 3, 2009It's between fifteen to twenty one cents of every dollar spent by hospitals. A recent study examined the costs of antibiotic resistant infections in hospitals. The main finding (italics mine):
The total attributable hospital and societal cost ranges for ARI in the expanded sample were as follows: hospital, $3.4-$5.4 million; mortality, $7.0-$9.2 million; lost productivity, $162,624-$322,707; and total, $10.7-$15.0 million. The total medical cost, if distributed to all sample patients, added $2512-$3929 (16.8%-26.3%) to the mean unadjusted hospital cost for all sample patients.
(An aside:…
mikethemadbiologist | October 20, 2009Last week, I was invited to give a talk at Stony Brook University's Ecology and Evolution department about genomics (very long time readers will know that I spent four years at Stony Brook as a post-doc and research professor). The talk was well received (thank you for asking) in part, I think, because of the way I began the talk.
I noted that, when I was at Stony Brook, a colleague and I spent roughly two years sequencing 10 genes from over 120 E. coli strains--and we were rightfully proud of what we had accomplished. At the time (2001-2002), this was one of the largest bacterial…
mikethemadbiologist | August 26, 2009You might find it hard to believe, but determining whether restricting antibiotic use leads to decreased resistance is actually not very straightforward. That's because antibiotic resistance genes can be linked to--that is, they travel along with--other resistance genes or even genes that are favored for some other reason. So even when an antibiotic is no longer used, the use of other antibiotics (or other antibacterials such as quarternary ammonium compounds or colloidal silver) can keep these genes around.
But quinolone antibiotics such as ciprofloxacin ("Cipro"), which are used to treat…
mikethemadbiologist | August 12, 2009In the midst of the concern about TEH SWINEY FLOO!, very few people (other than the Mad Biologist), have been discussing the double whammy of influenza followed by bacterial infections. A couple of years ago, I first started describing reports of KPCs:
No, KPC isn't a new fast food restaurant. It's short for Klebsiella pneumoniae carbapenemase. The bad news: it's very hard to treat. The good news: it's very rare...for now.
Actually, the correct term is KPC-possessing K. pneumoniae [these genes are now showing up in other bacteria], but we'll just use the slang 'KPC'--it's what all the cool…
mikethemadbiologist | June 12, 2009It's never made much sense to me why the pathogenic bacteria Salmonella and Shigella (which is really E. coli) have lost the ability to use lactose (milk sugar). In Shigella, we know that when we restore some lost functions through genetic manipulation (e.g., cadaverine production), they actually prevent these altered Shigella from causing disease. But lactose seems to be a good sugar to be able to grow on--they're exposed to it from time to time (in infants).
The genus Salmonella contains two species: S. enteriditis, which causes disease* and can't use lactose as a carbon source, and S.…
mikethemadbiologist | June 3, 2009...ok, I'll stop. But 99 E. coli commensal genomes will be sequenced. And that's really cool.
I'm always wary of counting chickens before they hatch, but I'm fairly certain at least 99 E. coli genomes will be sequenced (NIAID will continue funding, and more than fifty are already in various stages of sequencing).
And to a considerable extent, it's the Mad Biologist's fault. I'm the crazy bastard who thought of this and proposed it (obviously, many, many others are involved from sequencing to funding, and, last but not least, strain collections).
What makes this project unique is that…
mikethemadbiologist | June 2, 2009A recent post about the looming specter of bioterrorism by William Lind due to 'biohacking' seems overblown to me. But before I get Lind, what I find particularly disturbing about hyping a non-existent bioterror threat is that it makes combating infectious disease--the stuff that kills millions worldwide--much harder due to unnecessary regulations and restrictions. Onto Lind:
For years, I have warned in these columns and elsewhere that the future weapon of mass destruction we should most fear is not a nuke. Rather, it is a genetically engineered plague, a plague no one has ever seen before…
mikethemadbiologist | May 21, 2009...the signal peptide? Interesting. I'll start at the beginning.
One of the few bright spots regarding the problem of antibiotic resistance is that resistance typically infers a fitness cost to the bacterium, at least initially. In other words, the resistant strain usually grows slower than a nearly identical sensitive strain*. While compensatory mutations can lower or eradicate this 'cost of resistance', it is thought that resistance can't increase initially without favorable selective conditions--antibiotic use--due to the cost of resistance.
We'll need a little background about…
mikethemadbiologist | May 20, 2009While I'm away at ASM, here's something from the archives for you
When I read Olivia Judson's post about hopeful monsters, I didn't think she used the term correctly (here are some good explanations why), but I was surprised by Jerry Coyne's response.
First, the personal attack on Judson is unwarranted: when we reach the point where the serious challenge to evolutionary biology is the misuse of a discredited decades-old idea, as opposed to the politically powerful anti-science creationist movement, we're in a pretty good place. She made a mistake--I don't think her motives were self-…
mikethemadbiologist | March 23, 2009By way of ScienceBlogling Sandra Porter, we discover that Cofactor Genomics has announced that they will sequence some genomes for free to enable students to learn about genomics:
In response to a great post on Keith Robison's "Omics Omics" blog which highlighted how Next-Gen DNA sequencing platforms could change the science classroom as we know it:
http://omicsomics.blogspot.com/2009/03/next-level-in-genomics-term-papers.html
Cofactor will ask course organizers for a 1 page description of how their ~700Mb sequencing project could be used as an effective teaching aid in their class. We will…
mikethemadbiologist | November 28, 2008One of things I've done in my job is write letters of recommendation for various genome sequencing projects, particularly antibiotic resistance related projects, so it's always good to see that those letters might result in published work. So onto to an incredibly resistant Escherichia coli strain.
E. coli SMS-3-5 is a strain of environmental E. coli that is incredibly resistant to a broad range of antibiotics, to the point where the antibiotic does not go into solution. Of 33 antibiotics tested, only imipenem, meropenem, amikacin, gentamicin, and nitrofurantoin were effective against this…
mikethemadbiologist | October 14, 2008
How one views a recent article on the mortality due to antibiotic resistant infections depends on whether you're a glass half-full or half-empty type (me, I just worry about dropping the damn glass). A recent article in Clinical Infectious Diseases notes that there has been no change in the death rate due to antibiotic resistant infections in Staphylococcus aureus bloodstream infections, Pseudomonas aeruginosa pneumonias, and Escherichia coli urinary tract infections.
The authors conclude (italics mine):
We initiated this study to evaluate whether the impact of antimicrobial resistance on…
mikethemadbiologist | September 12, 2008New data show that antibiotic resistance genes travel together, at least in E. coli isolated from farms. Lookee, a picture:
(click to embiggen)
These are the major types of antibiotics. Anytime you see a "+", that means that a gene that provides resistance to some or all of the antibiotic in that class*. For example, the second "+" in the first column means that E. coli with a tetracycline resistance gene are more likely than those without a tetracycline resistance gene to also have an aminoglycoside resistance gene. And by more likely, it's usually five to fifty times more likely.
When…
mikethemadbiologist | September 4, 2008A recent paper examined if use of the antibiotic cotrimoxazole was correlated with resistance in three different bacterial pathogens, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. To quickly summarize, in one species, S. pneumoniae, resistance was correlated with use, whereas it was not for the other two species. While the study is fine for what it is, it inadvertently highlights a problem most surveillance systems have:
they don't incorporate genetic information.
Without genotypic information, we don't really know what happened. Is the correlation spurious,…
mikethemadbiologist | July 30, 2008
With all of the stories about bacterial contamination of food, a recent paper describes one possible way to reduce the virulence--the ability to cause disease--of the bacterium Escherichia coli.
Farms are an obvious...input of E. coli--the amount of feces that a single pig produces is staggering, never mind a thousand pigs*. The concern is that E. coli from agricultural settings can either serve as a genetic reservoir of virulence (disease-causing) genes (and antibiotic resistance genes too), or as a source of virulent E. coli strains, such as E. coli O157:H7.
What the authors of paper…
mikethemadbiologist | July 25, 2008I've written before about antibiotic resistance in the developing world. Because these poor communities don't have access to many antibiotics, one wouldn't expect high frequencies of resistance to antibiotics. Resistance to ciprofloxacin ('Cipro') is all the more shocking because these communities don't have access to this relatively expensive drug*. Not only is ciprofloxacin resistance observed, but, in these communities, it occurs at higher frequencies than in intensive care units in developed countries.
So what's a possible culprit?
Sadly, a recent paper in PLoS ONE suggests that…
mikethemadbiologist | July 6, 2008I'm surprised that I haven't seen a spate of posts from certain quarters proclaiming that the Lenski-Schlafly dustup is good for creationists. I think the assessment by RationalWiki is right on target:
Mr. Schlafly certainly intended that his letters to Prof. Lenski would have the effect of somehow discrediting his work or discomforting him in some way. In the event the consequences couldn't have been more different.
*As a result of Mr. Schlafly's tomfoolery he has raised the status of Prof. Lenski's evolution-demonstrating paper from the status of "Highly Significant" to "Internet Science-…
mikethemadbiologist | June 20, 2008So I emerge from my grant writing burrow only to discover by way of ScienceBlogling PZ that the clowns at Answers in Genesis are pestering National Academy of Sciences member Richard Lenski about the citrate evolution in E. coli paper he co-authored.
Fortunately, Gerlach at Off Resonance does a great job fisking this creationist crapdoodle, so I don't have to. While I'm glad Lenski responded, he should cut them off at this point. The problem is that his response, which is quite sensible--he presents the data that show that contamination is not an issue among other things--does not matter to…
mikethemadbiologist | April 15, 2008Well, it's a better title than "Duration of Stool Colonization in Patients Infected with Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae." What the authors were looking at is how long E. coli and K pneumoniae (another opportunistic commensal that is found in people at low densities) that carry resistance genes that encode enzymes known as ESBLs (extended-spectrum beta-lactamases).
ESBLs confer resistance to many of the antibiotics that start with "cef-" (or "ceph-") or that end in "-cillin" making these drugs ineffective at treating these infections.
On…