Dr. Cramer on August 27th, 2015

Can bacteria survive the freezer?

Bacteria will freeze along with the food they are on when they are stuck into a freezer. The pathogenic bacteria on foods that cause human disease  are primarily mesophiles or organisms that grow best at around 37 degrees Celsius.  In a freezer at -20 degrees Celsius, their bacterial enzymes cannot function because the water inside the cell has frozen, so they cannot grow. It has been reported that if you put a raw chicken into your freezer (considered a slow freeze), you may reduce the number of bacteria by approximately 90%. This is primarily due to the formation of ice crystals in the bacterial cytoplasm which then ruptures the bacterial cell wall and kills the cell, reducing the number of viable bacteria.  In many food processing plants, food is flash frozen in a way that fewer ice crystals form in the food so more bacteria survive as well (up to 70 percent survive as opposed to 10 percent).

So the problem is the exponential growth capacity of bacteria. If the food is thawed improperly, (at room temperature) surviving bacteria on the surface can quickly reproduce to pre-freeze levels (USDA source).  So when is this a problem?

Let’s use chicken as an example food. In a Consumer Reports article in 2013, chicken from retail stores around the country were tested and Salmonella was found on 10.8 percent and Campylobacter on 43 percent of all samples tested. Just this spring in the UK, they tested over 4000 samples and found that 73 percent of all chicken tested were positive for Campylobacter. Worse yet, of those,  19 percent were deemed heavily contaminated. So even ten percent of these organisms on the thawed bird would be a serious contamination issue.

The other way that we know that bacteria survive freezing is just to check the news and the various outbreaks of illnesses linked to frozen foods. There was an outbreak in March, 2013 of E. coli O121 that sickened 24 people in 18 states  linked to frozen chicken quesadillas. The most recent outbreak is actually ongoing, where they have linked raw, frozen, Stuffed Chicken Entrees by Barber Foods to a Salmonella outbreak that has sickened 9 people in four states. Not only have these people become seriously ill, but the CDC identified that the strain of Salmonella responsible for the outbreak is a multi-drug resistant strain impervious to both tetracycline and ampicillin.

Best case practices in the case of contaminated foods? For pre-cooked food such as the quesadillas, reheat according to directions on box. Bacteria are killed by reaching temperatures of 165F, even muti-drug resistant bacteria.

For raw food, such as chicken, make sure to use aseptic technique when handling the food. Don’t touch surfaces of the kitchen with hands that have come into contact with the bird. Watch where the juice from the thawed chicken lands (it will be full of viable bacteria). Don’t wash your chicken in the sink, it aerosolizes the bacteria, and they may land on other surfaces that you are not aware of. NPR had a nice overview of what to do if you want to brine your chicken or marinade,-just remember that this fluid has bacteria in it and be careful when you are pulling the chicken out as to where the water droplets go. Thaw food in your refrigerator, in cold water, or in brine.

I always have a dish of hot soap water ready and wash my hands a lot when handling raw chicken. I turn on my faucet to wash my hands with my arm. Washing hands with soap is sufficient to prevent contamination. I also have my sink empty and all counter surfaces clear so that if anything DOES land there, it is a simple soap and water clean up.

 

 

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A new outbreak of the strain of E. coli O157:H7 has just occurred in Canada. There have been just 12 cases, but all of the bacteria in those cases have exhibited the same genetic fingerprint, indicating an a common source epidemic (one that arises from a contaminated food source). Epidemiologists investigating the outbreak have not identified one food, but leafy greens.

The Public Health Agency of Canada is warning people to wash all food, keep refrigerated properly and use aseptic technique! From the article:

The following tips will help you reduce your risk of infection with E. coli or other food-borne illnesses:

  • Wash fresh fruits and vegetables before eating them, clean counters and cutting boards and wash your hands regularly.
  • Bacteria can grow in the danger zone between 4 °C and 60 °C (40 °F to 140 °F). Keep cold foods cold at or below 4 °C (40 °F) and keep hot foods hot at or above 60 °C (140 °F).
  • Keep refrigerators clean and at a temperature below 4 °C (40 °F). Install a thermometer in your fridge to be sure.
  • Place raw meat, poultry and seafood in containers on the bottom shelf of the refrigerator. Use containers that are large enough to prevent raw juices from dripping onto other food or touching other food.
  • Keep raw food away from other food while shopping, storing, preparing and serving foods.
  • Read labels and follow cooking and storage instructions for all food. When buying food, make sure to check the “best before” date, and if the product has expired, let the store know.
  • Use warm soapy water to clean knives, cutting boards, utensils, your hands and any surfaces that have come in contact with food, especially meat and fish.
  • Refrigerate or freeze perishable food within two hours of cooking.
  • Freeze or consume leftovers within four days of cooking. Always reheat leftovers until steaming hot before eating.

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Dr. Cramer on April 2nd, 2015

There is an outbreak of scarlet fever occurring in the UK. What makes this different from a regular Strep sore throat (caused by Streptococcus pyogenes) is that the strains of Strep causing these outbreaks encode a gene that allows them to produce a superantigen-exotoxin. This causes the non-specific activation of T helper cells, and creates the characteristic signs and symptoms of a sandpaper rash, and strawberry tongue.

But it is interesting how the signs and symptoms develop. First comes the typical Strep sore throat signs, a sore throat and a fever. Then, 12-48 hours after the first signs develop, the effect of the exotoxin becomes apparent, causing the effects of activation of non-specific T helper cells (the superantigen exotoxin binds outside of the antigen-binding site on the MHC class II molecule, allowing TCRs on T helper cells to non-specifically interact with these MHC molecules, and become activated.

The other thing to note, is that the effects of this toxin are relatively mild, and the threat to the child is the same as that of a regular Strep sore throat. In a patient under the age of 18, it should be treated immediately with antibiotics to prevent the Strep sore throat sequelae: Rheumatic fever or kidney failure, that occurs as a consequence of mounting an antibody response to specific strains of Streptococcus pyogenes.

 

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Dr. Cramer on March 11th, 2015

Yes, they have given an entire YEAR to celebrate phage and the discovery of phage 100 years ago! There are a number of articles that discuss the illustrated history of phage and how we may use phage to try to stop bacterial infections, as well as the beauty and diversity of different phages. For the last one make sure to scroll through all the images at the top of the article. Here is an example of the beautiful images created by the artist, Ben Darby:

Salmonella phage gifsy-23

Salmonella phage gifsy-23

From the Illustrated History of phage research:

If tailed phages on the planet Earth were laid end to end they would extend for 200 million light years?

It is also an illustration of where we may be going with phage technology as well!!

 

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Dr. Cramer on March 5th, 2015

Ok, some of you are off for spring break to a place that is sunny and warm (hopefully). But new research from Yale University published in the journal Science (Feb.20, 2015)  indicates that UV irradiation causes both direct damage (DNA dimer formation that causes mis-reading of a DNA strand) during UV exposure, but can also create reactive oxygen and nitrogen species (free radicals) that act on the melanin in our skin for at least 3 hours AFTER exposure to UV light. This damage happens with BOTH  sun exposure as well as tanning bed exposure- any UV exposure.

This data  indicates that melanin that protects us from the sun, may also cause cancer as well. This reinforces the notion that there is no such thing as a protective “base tan”. It is all DNA damage, plain and simple. And will continue to harm you long after you leave the sun.

So… on that note, I wanted to let you all know that sunscreens work! But sunscreens are water-resistant, NOT waterproof, or sweatproof.  Water resistant means that they will protect you for about 40 or 80 minutes in the water (depending on the type you purchased), but then have to be reapplied. Also, did you know that an SPF rating of 15 absorbs 93% of UV rays, and that 30% absorbs 97%? Any sunscreen rated higher than an SPF of 30 may be fudging their numbers, as it is almost impossible to stop more than 97% of UV rays. And with this in mind from the same article:

The rules also say only sunscreens with a sun protection factor higher than 15 can claim to reduce the risk of skin cancer, aging, and sunburn, and that those rated SPF 2 to 14 must be clearly labeled as not doing so.

So that means, if you use a sunscreen with an SPF of less than 15%, you are at risk for ALL of those: aging, cancer and sunburn.

So remember, have fun in the sun, but use a sunscreen of at least 15% and reapply often!!!

 

Happy spring break.

 

Dr. Cramer on March 2nd, 2015

Rob Knight is a pioneer in studying the human microbiome, and his TED Talk “How Our Microbes Make Us Who We Are” was all about just how important the microbiome is, how antibiotics may be altering important aspects of how it is supposed to function, as well as how he is using his lab to study how the microbiome changes over the course of a newborn’s life. It was amazing. I especially thought the aspects of how the microbiome makes us fat or thin was especially intriguing. I may stop dieting, and go searching for “skinny” microbiota….

As a matter of fact, it is so amazing, I signed up to become part of his research, the American Gut Project! For $99, I am getting my microbiome sequenced (using 16S ribosomal sequencing techniques). I will send him a sample of my microbiota (yes…that sample), and a detailed description of the food I eat, and what I do.

I will post more on the results when they come in!

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Dr. Cramer on February 27th, 2015

Leonard Nimoy stated that although he quit smoking 30 years ago, it had had a lasting impact on his lungs. It is reported that he died from the effects of Chronic Obstructive Pulmonary Disease (COPD ).  COPD is caused when toxins in the air you breath (especially from cigarette smoke) destroy the surface area of the lungs, reduces lung capacity. It is estimated that 80% -90% of COPD related deaths are due to smoking/toxins in the air from secondhand smoke. COPD is the third leading cause of death in the US.

From the NIH COPD website, people with COPD:

  • Have a shortness of breath while doing everyday activities.
  • Produce excess sputum.
  • Cough frequently, or constantly.
  • Wheeze.
  • Feel like they can’t breathe.
  • Are unable to take a deep breath. 

The best and easiest way to avoid COPD is to not start smoking. If you do smoke, stop. Also, your children will be impacted by your secondhand smoke if you smoke around them. Secondhand smoke takes away their health by your habit.

It is best to Live Long and Prosper.

Goodbye Mr. Spock.

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Dr. Cramer on February 7th, 2013

Bacteria are winning the antibiotic war, because we are giving them all the information they need to win.  How does this happen? Bacteria have been learning how to resist the antibiotics we have been taking for viral infections. ANTIBIOTICS CANNOT, DO NOT WORK AGAINST VIRAL INFECTIONS. Don’t believe me?

See the CDC Get Smart campaign:

Antibiotics do not fight infections caused by viruses like colds, most sore throats and bronchitis, and some ear infections. Unneeded antibiotics may lead to future antibiotic-resistant infections. Symptom relief might be the best treatment option.

or warnings from the  NIH:

If a virus is making you sick, taking antibiotics may do more harm than good. Each time you take antibiotics, you increase the chances that bacteria in your body will be able to resist them. Later, you could get or spread an infection that those antibiotics cannot cure.

Or alerts from the Mayo Clinic:

Antibiotics: Misuse puts you and others at risk

What are viral infections? According to the CDC, bronchitis is most commonly caused by a number of viruses, and only RARELY, bacteria

Causes of Bronchitis

  • Several types of viruses, most often:
    • Respiratory syncytial (sin-SIH-shull) virus (RSV)
    • Adenovirus
    • Influenza
    • Parainfluenza
  • Bacteria, in rare cases
  • Pollutants (airborne chemicals or irritants)

So based on the above, if you have bronchitis, antibiotics won’t help, and may actually hurt you.

Why is this important? Because bacteria are learning how to subvert the action of antibiotics and are spreading the message to other bacteria. We are losing our wonder drugs because…we think we can self diagnose and that antibiotics are useful in all situations.

Again, the words superbugs SHOULD alarm you.

Dr. Cramer on January 31st, 2013

In a very good article, USA TODAY describes how hospitals across the US are fighting a “Superbug” war. What is a superbug? It is a bacterium that has gained the ability to be resistant to almost all available antibiotics. The article discusses CRE bacteria. In class I have discussed the NDM-1 plasmid which encodes an enzyme called carbapenemase, which cleaves carbapenam antibiotics (which up until now had the been the antibiotic of last resort for extensively resistant bacteria). Both  CRE and NDM-1 are not examples of specific bacteria, but of genes that can transfer resistance to a wide array of bacteria.  Any bacterium containing the genetic information would be resistant. Examples are that both  E. coli and Klebsiella pneumoniae are identified as CRE bacteria.

How does this happen? The animation in the USA Today story is perfect. We take an antibiotic that a SINGLE bacteria may be resistant to. Then, that one bacterium can do one of two things. They can simply grow to fill in the spaces left by the sensitive bacteria, or they can use horizontal gene transfer to transfer antibiotic resistance to other bacteria that hadn’t been antibiotic resistant. Horizontal gene transfer is the ability of bacteria to share genetic information with other bacteria in a population. (Vertical gene transfer is what happens normally when a bacterium divides and replicates it genetic information for its daughter cells).  The animation details horizontal gene transfer with both transposons transferring resistance as well as conjugative plasmids via conjugation.

In class, we discuss that once a bacterium gains a conjugative plasmid, it WANTS to share the information with other bacteria. This can create an entire army of bacteria that are superbugs. Where is the best place for this to happen? The human gut is a great place for bacteria to get together and exchange information.

How quickly can this spread? According to the article:

the first known case, at a North Carolina hospital, was reported in 2001, CREs have spread to at least 41 other states

The NDM-1 was first identified in Swedish patient who had visited India for surgery in 2008 and bacteria containing this plasmid has been found in: 

India, Pakistan, the United Kingdom, the United States,Canada,Japan and Brazil.

Currently, CRE and NDM-1 bacteria are found primarily in hospital settings. But the concerns are that, similarly to MRSA, these organisms will become more common outside the hospital among the general population, creating a serious healthcare problem that won’t…can’t…be treated with any currently antibiotic therapy.

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Dr. Cramer on January 24th, 2013

There is a great  article in the online magazine Ars Technia  that details influenza viral replication and structure. It is essentially a re-print from a post from the epidemic of 2009 (there are a few details at the beginning regarding this year’s virus). However, what is there, is very good. It details how the virus replicates, what the H and N stand for in the viral names (hemagglutinin and neruaminidase) as well as how the virus infects.

If anyone in your family wants to know and understand influenza a little better this is a great article. One of the reasons I especially liked this article is because it details the fact that this is an RNA virus. More specifically, this virus needs not one, but requires THREE RNA dependent RNA polymerases (RDRPs) in order to make infectious virions:

Finally, the influenza virus’ genome exists as RNA, rather than DNA, and the (host) cell’s enzymes are not prepared to duplicate that or transcribe it into the messenger RNAs that get made into proteins. So, the flu virus brings its own, with three genes encoding RNA-dependent polymerases.

The article states that the best strategy for preventing the flu is a vaccine (killed or live attenuated), but that isn’t 100% effective (actually only 67% effective this year). If you do get the flu, this is a the best advise on what to do as holistic therapy in a  site  from the U.S. government:

You can treat flu symptoms without medication by:

  • Getting plenty of rest
  • Drinking clear fluids like water, broth, sports drinks, or electrolyte beverages to prevent becoming dehydrated
  • Placing a cool, damp washcloth on your forehead, arms, and legs to reduce discomfort associated with a fever
  • Putting a humidifier in your room to make breathing easier
  • Gargling salt water (1:1 ratio warm water to salt) to soothe a sore throat
  • Covering up with a warm blanket to calm chills

Little by little we are beginning to understand that Granny was WAY ahead of us in common sense treatments that actually work.