antibiotics

The peanut butter/peanut paste ingredient based salmonella outbreak has been in the news lately and we've discussed it here (and here, here, here, here, here). There are now about 500 reported cases and six deaths. That's a case fatality ratio of just over 1%. So what if there were a disease outbreak of 100,000 cases with a case fatality ratio of 20%? I think we'd be pretty alarmed. But it happened in 2005. And it happened in 2006 and 2007 and last year, 2008 And it's happening, now, too. It isn't salmonella or or even HIV/AIDS, although it is estimated to kill more people in the US than both…
I'm kidding, but ScienceBlogling Tara Smith has co-authored a PLoS One article about the emergence of the MRSA strain ST398 in Iowan pork farms. Pig farms are a tremendous reservoir of bacteria: as far as I can tell, there are about six pigs for every person in Iowa. MRSA ST398 a methicillin resistant S. aureus bacterium that has spread epidemic through various European animal populations (particularly pigs). It recently jumped from the animal population to the human population in Europe and has begun to establish itself there in hospitals. The last thing we want is for another MRSA…
The emerging MRSA strain ST398 has found a new home--chickens. MRSA (methicillin resistant Staphylococcus aureus) was first found to have swept through European swine herds from 2003-2006. Then it entered the hospital system. In the U.S., it had not been observed in agriculture until very recently (it's ScienceBlogling Tara's fault--on a serious note, she studies this critter). It hasn't been seen in hospitals in the U.S. yet. What's disturbing is that a recent study from Belgium indicates that MRSA is on the rise in chickens and that it's due to ST398 (this isn't a trivial thing; most…
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…
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…
Most people know that a good place to pick up an antibiotic resistant infection is in a hospital. Lots of pathogenic bugs there living (often) happily in a sea of antimicrobial agents. Better to stay away from hospitals, somewhere nice. But apparently, not at the beach: A drug-resistant germ linked to surgical wound and urinary tract infections was found on five U.S. West Coast beaches, according to scientists who said the bacteria isn't usually seen outside of hospitals. Samples of sand and water were taken from seven public beaches and a fishing pier in the state of Washington and southern…
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…
I've said this many times before, but it's worth repeating again: whether it's an influenza pandemic, or 'just' annual influenza (which, in the U.S., kills double the number of people as HIV/AIDS), what actually does the killing is the secondary bacterial infection, not the virus. A recent review describes the result of a large series of autoposies of victims from the 1918 pandemic (as well as later pandemics). The main finding (italics mine): Their findings are striking in the context of modern conceptions of the 1918 pandemic; the great majority of deaths could be attributed to secondary…
One of the most important things in public health is surveillance. While it's not sexy, you can't solve health problems if you don't have good data. Recently, many professional societies sent a joint letter to several representatives asking their support for the National Integrated Public Health Surveillance Systems and Reportable Conditions Act which will be submitted to committee (the full text of the letter is at the end of the post). The primary goal of the NIPHSSRCA (try saying that ten times fast....) is to modernize our surveillance infrastructure. When I would argue for electronic…
Suppose you were a cattle dealer and the US Food and Drug Administration, one of the federal agencies tasked with keep the food supply safe issued you a court order, twice, prohibiting you from putting your product into the food supply until you complied with a legally required record keeping system. The agency had their eye on you because the meat you produced had been found repeatedly to have illegal levels of antibiotics making it unfit for human consumption. But you didn't care and you violated the court orders. So the FDA went after you and you were found in criminal and civil contempt…
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…
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,…
A recent, must-read article for anyone concerned about the problem of misuse of antibiotics to treat viral bronchitis, not to mention anyone who prescribes antibiotics, was recently published in Clinical Infectious Diseases. The short version: giving patients antibiotics to treat viral pneumonia is dangerous for the patients themselves (never mind the evolutionary consequences of increasing resistance). Since antibiotics are almost never effective against bronchitis, the prescribing rate should be nearly zero, but in the U.S., 67% of adults with acute bronchitis received antibiotic therapy…
There are two excellent papers in the August edition of Emerging Infectious Diseases (open access) about influenza that suggest alternative (or parallel) ways of dealing with an influenza pandemic (note: by "alternative", I don't mean woo). The standard response that is typically discussed is an influenza vaccine--and I've mentioned before how important it is to increase our influenza vaccination surge capacity (not only is it good for dealing with a pandemic, but could serve as a source of vaccine production against the annual epidemic). There's a problem with this strategy. We can't be…
This is not good. A recent article in Emerging Infectious Diseases describes two separate cases of community-acquired ST398 MRSA--and neither case was associated with agriculture. Let me explain what this means and why this is really bad news. MRSA--methicillin resistant Staphylococcus aureus--is a serious problem: in the U.S., it kills more people annually than AIDS. Typically, the therapy used to treat MRSA is vancomycin, and strains resistant to vancomycin can't be treated on-label with any commercial antibiotics*. ST398 is a new clone of MRSA that is thought to be associated with…
I'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…
...seven years later? The bad news--for years, cephalosporin antibiotics (antibiotics derived from penicillin, such as ceftiofur, cephalothalin, cefoxitin, and ceftriaxone) were used 'off-label' (meaning irresponsibly) in agriculture (italics mine): Inspectors found a common antibiotic has been misused in animals through practices such as injections into chicken eggs and ordered farmers to stop the unapproved treatments because of the risk to humans. The drugs, called cephalosporins, were given in unapproved doses to chickens, beef, pigs and dairy cows, the U.S. Food and Drug Administration…
In a Journal of Infectious Diseases commentary about this article, there's a fascinating discussion of the relationship between the HTLV-1 virus, which can cause T-cell leukemia in about one percent of those infected, and gastric cancer caused by the bacterium Helicobacter pylori. And it's not what you would expect. Here's the summary (italics mine; references removed for clarity): In this issue of the Journal, Matsumoto et al. asked whether human T lymphotropic virus type 1 (HTLV-1) antibody status is associated with the risk of developing gastric cancer. In a cohort of >5000 patients…
I've noted before how stupid creationists are when they burble things like 'mutation is bad.' Well, a brief story in Nature once again shows just how stupid that whole idea is: Publishing in Chemistry & Biology Truman et al. have identified a single amino acid substitution in the active site of the protein Cep15, which is part of the glycopeptide antibiotic chloroeremomycin biosynthetic machinery in Amycolatopsis orientalis, that abolishes its catalytic activity. Reversing a point mutation in the cep15 gene produced a functional enzyme. This finding represents the first time that the…