microbiology
mikethemadbiologist | June 16, 2008
I've been saying for a while now that the 'piggy MRSA*', known as ST398, is going to be a problem. Always listen to the Mad Biologist.
Last week, I was talking to someone who is monitoring MRSA in the New York area, and they've seen two cases of ST398 MRSA in hospitals. This really shouldn't come as a surprise since ST398 is sweeping through the swine population. The only question now is will ST398 simply replace the predominant MRSA strains, or will it add to the total number of MRSA infections and deaths.
Of course, those aren't mutually exclusive possibilities...
*MRSA is methicillin…
grrlscientist | June 13, 2008tags: researchblogging.org, evolution, experimental evolution, adaptation, mutation, natural selection, Richard E. Lenski
The common gut bacteria, Escherichia coli, typically known as E. coli.
Image: Dennis Kunkel.
Evolution is a random process -- or is it? I ask this because we all can name examples of convergent evolution where very different organisms arrived at similar solutions to the challenges they are faced with. One such example is the striking morphological similarities between sharks (marine fishes) and dolphins (marine mammals). Thus, based on observations of convergent…
sporte | June 11, 2008Hey students: if you are looking for a summer internship in marine metagenomics and you can get your application together before June 16th, Jonathan Eisen posted information about an open position on his blog.
It also looks like he's looking for post-docs (see the side bar on the right of this page.)
sa smith | June 4, 2008This is a repost from the old ERV. A retrotransposed ERV :P I dont trust them staying up at Blogger, and the SEED overlords are letting me have 4 reposts a week, so Im gonna take advantage of that!
I am going to try to add more comments to these posts for the old readers-- Think of these as 'directors cut' posts ;)
So like, you know when people go all Monty-Burns-as-Howard-Hughes and start seeing germs everywhere?
I dont have that. But I kind of have that. Somehow, I work viruses into every aspect of my life... Including poop.
So I gotta say to PalMD:
Its not the bacteria! Its bacteria…
mikethemadbiologist | May 21, 2008An article in Emerging Infectious Diseases describes a joint collaboration between the CDC and Mexican health authorities that built a system to monitor the spread of Salmonella through the food chain and into people. One finding shocked me.
The authors examined four Mexican states, and the carriage of Salmonella in asymptomatic children ranged from 1.9% to over 11 percent. That's a lot of kids with Salmonella who are not exhibiting any symptoms:
Salmonella carriage was strongly correlated with contamination of meat by Salmonella* and by overall poverty. While the healthy kids had fewer…
mikethemadbiologist | May 20, 2008Two stories published in the New York Times today underscore the importance of handwashing in preventing infection. First, from a public hospital in New York:
Timeouts to wash hands and put on hairnets, a simple checklist to ensure that such seemingly obvious precautions are done, and advertising campaigns directed at everyone from the most senior doctors to the poorest of patients have been credited with drastically reducing the number of serious infections at New York City's public hospitals.
Since 2005, central-line bloodstream infections, which stem from bacteria invading a catheter…
neurophilosophy | May 17, 2008The brain is an organ of staggering complexity, consisting of hundreds of billions of cells (and tens of thousands of different cell types) which form millions of specialized circuits that are organized into thousands of discrete areas. Neuroscientists have a number of methods for investigating brain circuitry and the connectivity of neurons within circuits. One of these involves exploiting the abilities of certain viruses, such as the herpes viruses, to target nerve cells; genetically manipulated viruses can be used to trace the synaptic connections between cells. This method has its…
mikethemadbiologist | May 13, 2008According to a recent Applied and Environmental Microbiology paper, influenza viruses are able to survive on banknotes. Lookie, bar graphs:
(from the paper) Duration of infectiousness according to the size of the initial inoculum and the presence or absence of mucus. Influenza A/Moscow/10/99 (H3N2) virus was deposited in triplicate on banknotes at the following concentrations, each in the presence (H3m) or absence (H3) of respiratory mucus: (A) 8.9 x 10e5 TCID50/ml; (B) 4.4 x 10e5 TCID50/ml; (C) 2.2 x 10e5 TCID50/ml; (D) 1.1 x 10e5 TCID50/ml. (E) Similarly, influenza B/Hong Kong/335/2001…
mikethemadbiologist | May 8, 2008
Over at Shakespeare's Sister, I came across this link to an announcement of a new Chlorox disinfectant that is "a one-step, labor-saving solution for killing both strains of MRSA."
There seems to be some confusion here.
Let's start with the basics. MRSA is the bacterium methicillin resistant Staphylococcus aureus. Traditionally, MRSA has been classified into two kinds: CA-MRSA, community-acquired MRSA, and HA-MRSA, hospital-acquired MRSA*. A CA-MRSA infection is defined as an infection that occurs in a patient who has been in the hospital for less than 48 hours; in other words, they…
mikethemadbiologist | May 6, 2008While many of my fellow ScienceBloglings have discussed GINA (The Genetic Nondiscrimination Act), one other reason this is an important piece of legislation involves the Human Microbiome Project.
I've written about the Human Microbiome Project before, but, in a nutshell, it involves sequencing the microorganisms on us and in us. Basically, we take a biological sample--any collectable sample, preferably one that smells bad, and is icky and gross--will do, and sequence DNA from the sample. While some of the DNA will be microbial, much of it will be human (otherwise, DNA-based forensics wouldn…
mikethemadbiologist | May 4, 2008Several of my fellow ScienceBloglings have noted that the increase in measles cases is due to idiots who refuse to get vaccinated. Beyond the obvious health threat this represents, there is a more subtle, yet equally murderous effect of all of this anti-vax woo.
It distracts us from other vaccination programs that we need to institute. Every year, roughly 36,000 U.S. residents die from influenza--the 'boring' kind. Why this isn't viewed as a major health crisis, while breast cancer, which kills approximately the same number annually, is escapes me. Not because breast cancer isn't an awful…
mikethemadbiologist | April 30, 2008A recent article by National Institute of Allergy and Infectious Diseases (NIAID) staff emphasized that NIAID funds over $800 million annually to study antimicrobial resistance. I've heard this same argument many times, and, every time, people always grumble about how that money includes all microorganisms, as opposed to bacterial antibiotic resistance (NIAID never breaks the money down by organism). In particular, the ESKAPE organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanni, Pseudomonas aeruginosa, and Enterobacter species), most of which…
mikethemadbiologist | April 25, 2008From a long time ago on a blog far, far away (and now chomped by Blogger) comes this post about how responding to bioterrorism requires a public health, not security infrastructure.
Salon is running a story that claims the anti-war march of Sept. 24 might have been subjected to a botched tularemia bioterrorist attack. I have no idea whether or not this is correct. Nonetheless, it highlights something very important-an appropriate and adequately funded public health response to bioterrorism is needed, since it is often impossible to distinguish between terrorist attacks and natural outbreaks…
mikethemadbiologist | April 24, 2008An outbreak of vancomycin resistant MRSA, or VMRSA, would be the 'perfect microbiological storm', even worse than vancomycin resistant Staphylococcus aureus (VRSA). The only currently available antibiotics that would be effective against it would have to be used off-label, and are not very effective against sepsis (bloodstream) infections. Fortunately, VRSA is observed only anecdotally: a single patient, usually on long-term vancomycin therapy, is infected with it, and it is not spread to other patients or healthy people.
One reason is that most patients with VRSA are already in hospitals…
sporte | April 17, 2008In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions.
We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different ribosomal RNA genes. Many species of bacteria have multiple copies of 16S ribosomal RNA genes and the copies can differ from each other within a single genome and between genomes.
Now, in one of our last projects we are determining where…
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…
grrlscientist | April 13, 2008tags: hamster, PetSmart, lawsuit, lymphocytic choriomeningitis virus, LCMV, zoonosis
Portrait of a murderer:
A Siberian dwarf hamster, Phodopus sungorus.
Orphaned image.
I just learned that a lawsuit was recently filed in Massachusetts Superior Court on behalf of a man who died one month after receiving a transplanted liver that was later determined to be infected with lymphocytic choriomeningitis virus (LCMV). Apparently, the organ donor purchased a pet hamster from a PetSmart in Warwick, Rhode Island, and this hamster was later shown to be infected with this deadly virus.
LCMV is…
grrlscientist | April 12, 2008tags: What Bugged the Dinosaurs?, dinosaurs, insects, disease, George Poinar, Roberta Poinar, book review
I grew up with a fondness for dinosaurs. Their unbelievable size, their peculiar shapes, and their undeniable absence from the world as I knew it were all sources of fascination. But never once did I think of the dinosaurs as being plagued by biting insects and other blood-sucking arthropods; mosquitoes, flies, ticks and mites were creatures that haunted camping trips, picnics and attics, not the majestic dinosaurs! But according to the new book, What Bugged the Dinosaurs? Insects,…
mikethemadbiologist | April 10, 2008Several people have argued that if an influenza pandemic were to occur, it will rapidly evolve to become less virulent--that is less deadly. A recent paper explains why this might be wrong.
Basically, the flaw with the 'optimistic' argument is that it is assumes that the virus will be optimally fit given its environment (lots of fat, juicy hosts to kill). As it starts to kill off its hosts, its virulence (ability to make dead people or 'deadliness') and transmission rate (ability to infect new hosts) will decrease to another optimal point where the virus will be able to maximize its…
mikethemadbiologist | April 9, 2008While many laboratory experiments have shown that antibiotic resistance imposes a fitness cost on resistant bacteria, it's far less clear if this is the case in natural populations. In Europe, the phasing out of a vancomycin analogue, avoparicin, resulted in a dramatic decrease in vancomycin resistance in enterococci bacteria, from roughly seven percent to about three percent. However, the drop doesn't appear to have continued further (although the economic and health burdens of treating vancomycin resistant enterococci make this decrease a good thing).
One of the problems with most studies…