microbiology

One of the key biological questions about antibiotic resistance is to what extent is the spread of resistance due to the evolution of new resistant strains versus the spread of existing resistant strains. With MRSA (methicillin resistant Staphylococcus aureus, it's been thought that epidemic spread of a few resistant genotypes (strains) is responsible for much of the increase in MRSA, as shown by this image of pulsed field gel electrophoresis (PFGE) done on a nationwide collection of MRSA: (from here) However, methods such as PFGE lack the genetic resolution to determine if gene transfer is…
One 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…
I suppose I'll have to start at the beginning. One of the things we do in the microbiome project is analyze microbial communities by assessing the diversity of 16S DNA sequences*. In other words, we want to know what species or 'operational taxonomic units'--OTUs--are present and how many of that OTU are there. Operationally, we are taking a bunch of DNA sequences and placing them in categories. This, of course, is more difficult than it sounds. One of the issues with 16S is that many (nine to be exact) regions of the gene are hypervariable--they evolve so quickly that these regions can't…
This wasn't in the lab, but it was an accident, and it was funny later on. Normally, I wouldn't think twice about storing bacterial cultures in a refrigerator. After all, bacteria on a petri plate, inside of a plastic bag, are kind of stuck. They can't get out of the plates, and even if they did, they certainly can't crawl out of a plastic bag. I thought soil bacteria, on agar plates, were mostly harmless. Reposted from DigitalBio's greatest hits.Technorati Tags: humor, bacteria, taste, funny, tasting, food, Streptomyces When my husband was finishing graduate school, he brought home some…
There's a neat Discovery News article about Gromia sphaerica, a very large testate amoeba: A distant relative of microscopic amoebas, the grape-sized Gromia sphaerica was discovered once before, lying motionless at the bottom of the Arabian Sea. But when Mikhail Matz of the University of Texas at Austin and a group of researchers stumbled across a group of G. sphaerica off the coast of the Bahamas, the creatures were leaving trails behind them up to 50 centimeters (20 inches) long in the mud.... At up to three centimeters (1.2 inches) in diameter, they're also enormous compared to most of…
Fox 10 News has a rather gruesome story about the removal of a live parasitic worm from a woman's brain, which is accompanied by a film clip  containing footage of the surgical procedure. As the film explains, the woman, who lives in Arizona, first started to experience flu-like symptoms, followed by numbness in her left arm which grew progressively worse. Neurosurgeon Peter Nakaji operated, expecting to find a tumour in the brainstem, but instead found and removed a tapeworm. It goes on to say that the woman was infected either by eating uncooked pork or unwashed food contaminated…
I'm sure everyone else thinks the big news today is the announcement by the Washington State Health department requiring hospitals to report MRSA cases to the state. I think the cool news is their on-line database. We'll get to that a bit later. What is MRSA? MRSA stands for methicillin-resistant Staphylococcus aureus. It's a serious pathogen that causes skin infections and greater damage if it enters the body. The Seattle Times report - a quick summary For the past three days the Seattle Times has been running a series on hospital-acquired cases of MRSA. According to the report, 6…
Hospital cases of methicillin resistant Staphylococcus aureus (MRSA) have risen 33-fold during the past ten years in Washington state, yet our hospitals fail to identify or track cases in a systemic fashion (Seattle Times). The Seattle Times began a three-part investigative report today describing the rise in MRSA incidence, the consequences for patients, and the failure on the part of our hospitals to take measures to address the problem. According to the Seattle Times, six out of seven people get MRSA infections at some kind of health care facility. The spread could be contained if…
A recent paper in the Proceedings of the National Academy of Sciences suggests that the gut bacterium Faecalibacterium prausnitzii reduces the recurrence of ileal Crohn's disease. In the study, the authors determined that the percentage of total bacteria that were F. prausnitziii found in the ileal muscosa was roughly five percent in patients who did not have recurrence of symptoms six months after surgery versus roughly 0.1% in those patients who had symptoms six months later. When F. prausnitzii was grown with cultured intestinal cells, it was found to have an anti-inflamatory effect.…
The Harbingers of the Apocalypse NOW!! Actually, it's pretty good (and it's publicly available as a pdf). ScienceBlogling Revere has a good summary.
ScienceBlogling Revere links to a news article about high levels of VRE, vancomycin resistant enterococci in beach sand. While Revere and the article both describe how this indicates that VRE are established in the community, I think a far more chilling problem isn't mentioned at all: VMRSA. What's VMRSA? Vancomycin resistant MRSA (methicillin resistant Staphylococcus aureus). Every instance of VMRSA has involved an MRSA strain acquiring a plasmid (mini-chromosome) from a VRE strain. So far, most of these cases have occurred in Michigan. Apparently, the VRE strain that carries this…
I probably shouldn't find this amusing, but... Back a few years ago, a friend of mine worked at a biotech company in Seattle that had large windows looking out onto Puget Sound. They always cheered when the Navy ships came in, 'cause they knew it meant they'd have more work. Tom Joe has a funny post about the same topic, with a different twist. He's not talking about learning your status through any sort of laboratory test. He suggests using e-mail. UPDATE: Since Bora pointed out the PLoS article in the comments, I thought I should add some of the pictures from the article. I love the…
What happens when a group of streptococci stick to cells in your throat and start to make toxins? Your body fights back by making clones. The animated video, Fighting Infection by Clonal Selection, from Etsuko Uno and Drew Berry is so good that if I didn't know better, I would almost think it's really capturing clonal selection on film. What is clonal selection? We call this process "clonal selection" because only some lucky cells get selected for cloning. These cells have proteins on their surface that are able bind to bits of stuff from bacteria or viruses. We call that stuff "antigens…
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…
tags: DonorsChoose2008, education, public school education, fund raising, evolution education, nature education, bird education Mrs. G is seeking supplies for a microbiology lab. I, as a microbiologist, recognize the value (and the intense fascination!) of teaching students about the natural world, particularly microbes! I teach 7th grade Science in a school where the majority of the students are classified as Title 1, meaning that they need remedial help with their basic skills. Even without that classification, students this age are hard to motivate, especially in the content area of…
HealthMap is a great site that could be an excellent resource when teaching a biology, microbiology, or health class. Not to mention, I can picture people using it before they travel somewhere or even just for fun. I learned about HealthMap awhile ago from Mike the Mad Biologist, but I didn't get time to play with the site until today. Here's an example to see how it works. How do I use HealthMap? I begin using HealthMap by changing the number of diseases selected to "none." Then I scrolled through the list until I found something interesting. I chose "Poisoning." The number of…
If you like cool and unusual photos be sure to take a look at the 2008 Nikon Small World competition site. You can view lots of lovely pictures of things found under a microscope and vote for your favorite ones. You don't even have to focus the microscope! One of my favorites is the tubeworm larva. It looks something from outer space. There's even a contest to identify some of the more unconventional images. I only got three out of five. ;-( You can find them at www.nikonsmallworld.com
New 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…
One of the reasons to study the human microbiome--the microbes that live on and in us--is that many diseases might have a microbiological component. One of the best examples of this are gastric ulcers, most of which are caused by an infection by the bacterium Helicobacter pylori. A recent report by the American Academy of Microbiology argues that Mycobacterium avium subspecies paratuberculosis, also known as MAP, may, in part, be responsible for Crohn's disease: Because the bacterium Mycobacterium avium subspecies paratuberculosis (MAP) causes a Crohn's-like gastrointestinal disease in…
A 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,…