Research posted in PNAS last week identifies a family of retroviruses that may be involved in Chronic Fatigue Syndrome (CFS).  The new research identifies viral DNA in patient samples:

32 of 37 (86.5%) compared with only 3 of 44 (6.8%) healthy volunteer blood donors.

This confirms a study published in Science that a class of retroviruses (MLV-related viruses) may be involved in the disease. The take-home message from these two studies is that researchers found traces of this virus in the majority of patients studied, and very rarely in healthy controls.

However, other studies conducted in the UK and the Netherlands,  found no correlation between CFS patients and MLV-related viral infections.  And more confusingly, a study posted in the Journal of Retrovirology by the CDC in July stated that there was no correlation in patients from the US .

So what does this all mean? Well, at this point, it means we don’t know why there is conflicting data. The PNAS paper does a nice job of detailing what the problems may be. There may have been a problem in the CDC study in that the patients were not properly diagnosed with CFS (some individuals tested may have had depression or another infection that can mimic some symptoms of CFS). There may be some geographic restrictions as to where the virally associated CFS is occurring. Finally, the differences in the way the testing was conducted in each study may have played a large role in the difference of outcomes (most were PCR studies and different primers have different detection capabilities). Scientists are now working out more uniform experimental procedures and  guidelines for testing whether or not there is a real CFS association with MLV-related viruses.

There is a strong enough link that blood banks are discouraging CFS patients from donating blood as a precaution just in case the disease may indeed be due to an infectious agent.

But there may be real hope on the horizon for understanding, treating and limiting the spread of this disease.

That chickens may have salmonella in this setting should not shock you. The USDA states that humans and most animals (even chickens raised in organic settings) may be carriers of salmonella  (especially the strain Salmonella Enteritidis). It is just more likely that chickens in close, crowded conditions can spread the infection more easily to other chickens. I also love that the CNN article from above stated:

Chickens can pass the bacteria to eggs because the eggs leave hens through the same passageway as feces, according to the U.S. Department of Agriculture’s Food Safety and Inspection Service. Alternatively, bacteria in the hen’s ovary or oviduct can get to the egg before the shell forms around it, FSIS said.

The bad news is that it appears most people do not understand the egg laying process. Where do they think the eggs come from? The good news is that most people who get salmonellosis (fever, diarrhea, vomiting) from Salmonella Enteritidis will recover without treatment. This means you simply get better, no need for antibiotics.

BUT, that outbreak is not the point of this post. There has been another outbreak of salmonellosis. The latest outbreak occurred in Illinois from eating contaminated PICKLES. Of the 6 people who were infected, five where hospitalized.  I KNOW.  This is now officially “Scary Bacteria Month” (my designation). First, gram-negative superbugs, O157:H7 E. coli, millions of salmonella-tainted eggs and now bacteria that can live in a vinegar/salt solution (the term pickle is derived from the Dutch word pekel, meaning brine).

Salomonella should not be able to live in this environment. The pickling process should effectively destroy the organisms. Heat plus acid usually does the trick. However, the report I received stated in an abstract at the bottom that there is a growing incidence of outbreaks from acid-resistant food borne pathogens:

Outbreaks of acid-resistant foodborne pathogens in acid foods with pH values below 4.0, including apple cider and orange juice, have raised concerns about the safety of acidified vegetable products.

It appears that we may need to heat these foods, at longer temperatures to reduce these bacteria to safe levels.

My only reaction to this news is that it appears to me that we are developing a league of (evil) bacterial superbugs. What’s next? The ability to spin spider silk? Yikes.  But so far they are still  unable to swing from rooftop to rooftop, or leap the tallest building in a single bound. So we have that going for us.

The Lancet is reporting that there is a new antibiotic-resistant superbug out there. Yes, it does seem we have talked about  gram negative superbugs before.  But now they have identified a new enzyme being produced by bacteria that takes away our last and most effective weapon in our arsenal against these organisms.

The enzyme is called NDM-1 (which stands for New Delhi metallo-β-lactamase). This enzyme is capable of inactivating the antibiotic, carbapenem. Carbapenem antibiotics are THE antibiotics physicians go to when there are no other antibiotics left to treat infections with extensively antibiotic resistant bacteria.

What is especially scary is that this enzyme is now encoded on a plasmid. Plasmids can be transferred from one organism to another during bacterial conjugation. This means that bacteria that are NDM-1 positive can transfer that resistance to any other bacteria it comes into contact with.

It is also hypothesized that this enzyme evolved in bacteria in the India/Pakistan region and is being brought back to countries of origin by cosmetic surgery tourism . Individuals travel to India or Pakistan for routine cosmetic surgery, pick up a little bacterial passenger (in their gut) and bring it back to their country of origin. The NDM-1 bacteria can then be disseminated to others in those countries, creating a global outbreak. From the BBC article:

At least 17 of the 37 patients they studied had a history of travelling to India or Pakistan within the past year, and 14 of them had been admitted to a hospital in these countries – many for cosmetic surgery.

Of course, there is much information coming from India  denying NDM-1 originated there (as well as outrage at naming the enzyme after New Delhi).

The health ministry said it was unfair to link the bug to India and officials described it as “malicious propaganda”.

Today there is a report describing the first death from NDM-1 seen in continental Europe, in which a Brussels man succumbed to infection with NDM-1.

“The epicentre of the presence of this bacteria seems to be India and Pakistan, but it appears through contact and travel, its spread is becoming wider,” said Youri Glupczynski from the University of Leuven.

I saw an article on how to prevent the spread of this organism. The poster’s first response was to advise not to travel outside of the US. I am going to politely disagree. I think NDM-1 is here, and brewing. I predict we will see the first US cases of it in the near future.

So, should I stop posting about looming problems associated with improper use of antibiotics in our culture and the resulting problems that this creates?  I think posting about emerging antibiotic-resistance  may be a moot point, because  the Problem (with a capital P) is here and is  knocking at our door.

The reason why ground beef is so problematic is that people do not fully cook their ground beef. The bacteria present on the side of beef after processing gets ground into the entire batch. This is different from a steak. The surface of the steak  may be covered in bacteria but those are incinerated while cooking. The interior of the steak is not contaminated, so eating a rare steak is acceptable.

However, the interior of a hamburger is a lovely place for growing bacteria. If the hamburger is not cooked to an internal temperature of 160°F, the living bacteria in the middle of the burger are consumed, get into your intestine and start replicating.

After establishing their niche in your gut, this specific strain of E. coli (identified by its capsule and flagella) starts producing a toxin that can cause disease, such as gastroenteritis, but more specifically Hemolytic Uremic Syndrome (HUS). The secreted toxin  targets and destroys red blood cells, which can then shut down kidney function. This especially targets children under the age of 5 and the elderly:

More than half of children with HUS develop acute kidney failure. With kidney failure, the child’s urine output decreases. The urine may also appear red. Urine formation slows because the damaged red blood cells clog the tiny blood vessels in the kidneys, making them work harder to remove wastes and extra fluid from the blood. The body’s inability to rid itself of excess fluid and wastes may in turn cause high blood pressure or swelling of the face, hands, feet, or entire body.

The problem is that some individuals insist on eating (and feeding their children) undercooked hamburgers, which they say taste better. These people generally like to cook, consider themselves foodies, and pride themselves on their grill mastery. According to the article and to the U.S. Department of Agriculture’s Food Safety and Inspection Service (FSIS):

The only way to be sure ground beef is cooked to a high enough temperature to kill harmful bacteria is to use a thermometer to measure the internal temperature.

And yes, most of the time we see the contaminated meat coming from large food processing plants, but that doesn’t mean that your locally grown beef may not be also contaminated with the same organisms. Infections in cattle are subclinical, so the cattle do not display any outward symptoms that  they carry this strain of bacteria. In 2006, there was a large recall of organic beef that was contaminated with O157:H7.

So, foodies, beware. That rare hamburger could be a source of a lot more than just bragging rights.

Commensal bacteria are those organisms that live in our gut and protect us from colonization by harmful bacterial pathogens. By now, you all know how important gut flora is.  If not from articles in health magazines, then from the huge marketing onslaught that encourages us to eat food containing probiotics. Especially probiotics. They have even added probiotics  to dog food.

One important group of probiotic bacteria is the genus Bifidobacterium.  These bacteria are found in the healthy human gut, and are being added to all sorts of foods that tout probiotic benefits, such as yogurts (Activia) as well as dietary supplements.

The researchers  at U.C. Davis have found a specific subspecies of this bacteria,  Bifidobacterium longum, in breastfed babies. This subspecies has a unique set of enzymes that can break down complex sugars found in breast milk that the babies cannot use. The bacteria then grow and colonize the intestinal tract of newborns. This protects the newborns intestinal tract from colonization by pathogenic organisms because they then have no place to live.

Also, these sugars provide a secondary defense from pathogens by binding to receptors on some bacteria and viruses and preventing them from attaching to surface receptors found in the intestinal tract.

The complex sugars were long thought to have no biological significance, even though they constitute up to 21 percent of milk. Besides promoting growth of the bifido strain, they also serve as decoys for noxious bacteria that might attack the infant’s intestines.

However, since this strain of bacteria is only found in newborns and not adults, the researchers are not yet sure where this strain of bacteria are coming from.

The other big take-home message from this article is that although we may not understand why, most components of breast milk are probably important (I want to insert a DUH here but will refrain). And breast feeding takes on a bigger and more important role with every discovery about components of breast milk that we have not been able or interested in replicating in commercial baby formula.

“So for God’s sake, please breast-feed.”

Last week we discussed the dramatically higher incidence of VRE in Sweden. Today there is a report out from the Infectious Disease Society of America (IDSA) about a new strain of E. coli they are describing as the next superbug. This new stain is ST131, and  has been identified as the cause of 67-69% of all E. coli hospitalizations. The article states that with the acquisition of one more resistance gene ST131 will become essentially untreatable.

What is even scarier is how they describe this new strain:

In the past, highly virulent E. coli strains usually have been susceptible to antibiotics, while highly resistant strains have been fairly weak in terms of their ability to cause disease.  The susceptible strains were easily treated even though they caused serious infections, while the resistant ones tended mostly to affect only weakened or vulnerable individuals. Now, the study’s findings suggest, the ST131 strain has appeared with a high level of virulence and antimicrobial resistance.

They also do not know the source of ST131, so are having a hard time stopping the spread of this organism.

We need to realize that these very real monsters are going to become much more scary in the near future than any of the fictional vampires or werewolves we appear to be obsessed with.

A recent report out of Sweden is describing the growing incidence of vancomycin resistant enterococci (VRE) in hospital patients.   And by growing, I mean exploding. In the report, they stated that from from all of 2000 until 2006 they saw a total of 197 cases of patients that were colonized or infected with VRE. From July 2007 until February 2009 they saw an astounding  total of 760 cases reported.

How does E. facalis gain the ability to resist treatment with vancomycin? It obtains a plasmid that confers high level resistance to this antibiotic. This is a problem because gut bacteria can conjugate and spread the plasmid to other organisms that live in the gut. (E. coli, another gut resident,  is gram negative and therefore already innately resistant to treatment with vancomyin).

Additionally? Enterococci are either innately resistant to or have acquired resistance to:

penicillinase-susceptible penicillin (low level), penicillinase-resistant penicillins, cephalosporins, nalidixic acid, aztreonam, macrolides, and low levels of clindamycin and aminoglycosides. They use already-formed folic acid, which allows them to bypass the inhibition of folate synthesis, resulting in resistance to trimethoprim-sulfamethoxazole.

Enterococci also have acquired resistance, which includes resistance to penicillin by beta-lactamases, chloramphenicol, tetracyclines, rifampin, fluoroquinolones, aminoglycosides (high levels)

The presence and increasing incidence of antibiotic resistant bacteria should be making us all much more conscious of how and when we use antibiotics.  The problem? We think we know when and how to take antibiotics.

More on this tomorrow…

But as beautiful as they are, my favorite quote was from the article’s author regarding the artist and his sculptures and science:

he groused in a way that would endear him to any grumpy science-journalism hack.

“I’m just now on the front page of one of the Nature journals,” he said. “But they used one of my swine flu sculptures to illustrate H.I.V. You’d think they would have known better.”

Thanks to Brandy Dykhuizen  for the article.

And on top of all that goodness, recent research presented at the ASM (American Society for Microbiology) meeting in San Diego is telling us that some bacteria can actually MAKE YOU SMART and HAPPY!  Really.  Not all bacteria, but a  specific common soil bacteria found everywhere, called Mycobacterium vaccae.

In 2007, scientists demonstrated that this bacterium, when used as a vaccine, can have effects on humans that are similar to those seen with antidepressants (by increasing seratonin levels in the brain). The current study (in which mice were fed these bacteria) demonstrated that the mice eating M vaccae learned faster and were less anxious than controls not receiving the bacteria. If the mice stopped receiving the bacteria they lost the edge they had gained on the control animals.

It is interesting to think of people taking pills filled with bacteria daily to get this effect. But you have access to this breaking science right now. This your prescription: Go outside and get those hands dirty, and play in the mud!

The latest illness associated with drinking raw milk involves an outbreak of campylobacter infections in Utah.  Symptoms of infections with Camyplobacter jejuni?:

mild to severe infection of the gastrointestinal system, including watery or bloody diarrhea, fever, abdominal cramps, nausea, and vomiting.

Earlier, there had been an outbreak of salmonella linked to the same dairy. Yes, I know, it is essentially the dairy’s responsibility, but I am just reminding you, you can get sick from drinking raw milk. Other outbreaks associated with raw milk consumption have included E. coli O157:H7 as well as listeriosis.