Dr. Cramer on October 10th, 2016

These are not aliens, but a newly recognized type of bacteria found in the deepest regions of earth.

In class, we divide bacteria into categories depending on their growth and energy requirements.  One such division depends on where the bacteria derive their energy. Some bacteria obtain energy from sunlight, and are known as phototrophs (photo: light, troph: obtaining nutrition/energy). Bacteria that utilize organic materials are known as chemotrophs. And we thought that was it…until a recent discovery  found bacteria that derive their energy from the radioactivity produced from uranium!

The name of the organism is Desulforudis audaxviator, and it was found in a gold mine. The bacteria harvest molecules that have been energized by being split by radioactivity.  The bacteria take in the energized molecules, extract the energy and eject the spent molecule back out. So, would this then make this organism a radiotroph?

The scientists in this article are also hypothesizing that life like this could grow on planets without much of an atmosphere where these bacteria could grow on galactic cosmic rays (GCRs). They used Mars as a possible place for these organisms to exist. Some people are calling these alien organisms, but I like to think of them as an example of just how amazing life on earth can get.

Maybe our next search should be for silicon based life forms that grow on radiation? At this point, I think anything is possible!


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Dr. Cramer on September 9th, 2016

Thanks to MCRO student Jack Iasiello for sending me a link to a fascinating video of how E. coli can quickly evolve antibiotic resistance. Harvard University and the Technion–Israel Institute of Technology set up a 2 foot by 4 foot “petri dish” of agar with increasing antibiotic gradients of either ciprofloxacin or trimethoprim. Then, set up a video and watched what happened… Link to article and video.


(Spoiler alert!! It took only 12 days to evolve resistance to even 1000x the normal dose that inhibited the initial strain). They also were able to track the specific strains that were evolving this resistance.

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Antibiotic resistant strains of Shigella sonnei are showing up around the world, US, Australia, Europe and Asia. Researchers in Vietnam have been able to track isolates from a survey of resistant organisms identified around the world to a specific clade of bacteria that appears to have developed  in South Asia. A clade is “a group of organisms believed to have evolved from a common ancestor“. This particular strain of S. sonnei has common mutations in its genetic code that has indicated a common clonal emergence (all the bacteria in the study were investigated using whole genome sequencing).

It appears that 80% of the isolates studied were obtained from travelers to India.  This particular strain of S. sonnei had developed multi-drug resistance but have specifically developed resistance to the type of antibiotics known as fluoroquinolones, with the antibiotic Cipro, being the most notable member. Cipro is the most commonly prescribed antibiotics for a S. sonnei gastroenteritis.

Sexually transmitted diseases (STDs) are making an unwelcome comeback all across the United States. We are seeing especially problematic increases in syphilis, gonorrhea and chlamydia.

What is behind the amazing increase in disease? It is thought to be due to the fact that HIV is now becoming a manageable disease thanks to PReP, and HAART therapies, as well as due to the rise of apps like Grindr and Tinder for quick anonymous hookups.

What kind of increases are we seeing?

  • California:
    • Santa Barbara, reports indicate that there were only 10 cases of syphilis in 2012, and almost 40 cases in 2015. Gonorrhea doubled in 2015 (from 170 in 2012 to 334 cases in 2015).  There were over 2300 cases of Chlamydia in 2015 as well (up 20%).
    • Bakersfield had 28 babies diagnosed with congenital syphilis, with 6 children dying from the infection.
  • Illinois:
    • the number of cases of syphilis rose from 1,682 in 2014 to 1,974 in 2015;
    • chlamydia cases rose from 66,593 in 2014 to almost 70,000 cases in 2015,
    • gonorrhea rose from  15,971 cases in 2014  to 17,130 in 2015.
  • Indiana:
    • Had a 70% increase in syphilis, from 297 cases in  2014 to over 500 in 2015.
  •  Texas:
    • Lubbock County Texas is under a syphilis alert due triple the number of cases as of the end of April of 2016 as there were in all of 2015.
  •  Las Vegas:
    • Saw an increase of  128% in the number of cases of syphilis from 2014 to 2015
  • Maine:
    • There were 3993 cases of chlamydia reported  in 2015 and 422 cases of gonorrhea. Based on numbers in for the first four months of the year,  Maine is on track to surpass both those numbers in 2016.

and finally:

  • Wake County, NC:
    • There was a 40% increase in cases of syphilis from 2014 to 2015.

The main populations where the increase is being detected in the highest percentages is in young adults and homosexual men.  If you think that this is a problem only in America, there are also reports of the same thing happening in the UK, Sweden, Japan and Australia.

The majority of the time, these diseases can be treated with simple antibiotic therapy, but if untreated can lead to serious problems. Gonorrhea and chlamydia can cause pelvic inflammatory disease, and infertility. If untreated, syphilis can cause blindness, neonatal disease and even death.

Word has got to go out. Young people and gay populations CAN control this with simple common sense precautions like condoms or knowing your sexual partner.

Safe sex is not something that should be thought of as only something reserved for HIV.

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Dr. Cramer on December 1st, 2015

There have been over 2000 cases of Syphillis documented in Japan by the end of Oct., 2015. This was up from around 1600 cases in all of 2014.

The main cohort of infected individuals? Females in the 20 to 24 years age group.

One of the main reasons sited for the increase in this demographic is declining risk of contracting HIV.

To read the entire article, click HERE

Dr. Cramer on October 7th, 2015

Dr. Aziz Sancar, just won the Nobel Prize for chemistry today, along with two other scientists,Dr.Tomas Lindahl from the Francis Crick Institute and Clare Hall Laboratory, and Dr. Paul Modrich, from Duke University.  All study different mechanisms of DNA repair. The coolest thing is that my micro class just studied all three repair mechanisms. One of the things Dr. Sancar stated in the news conference at UNC, that an understanding of how DNA gets mutated, and how the cell fixes these mutations, is integral in understanding the foundations of cancer, as well as the establishing an understanding of a treatment for cancer.

Dr. Sancar studies the mechanism behind UV (sunlight damage) called thymine dimer repair, called excision repair (link to Youtube animation).

Dr. Modrich studies the mechanism behind mismatch repair (link to Youtube animation)

Dr. Lindahl studies the mechanisms of repair behind oxidative damage, called base excision repair.

Dr. Aziz Sancar discussing his Nobel Prize in Chemistry at UNC Marsico Hall

Dr. Aziz Sancar discussing his Nobel Prize in Chemistry at UNC Marsico Hall


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A new study published in the journal Science Translational Medicine  and discussed in the journal Science this week illustrates the importance of a normal microbiome and what changes in your microbiota may mean for long term health.

To look find associations between microbiota and disease, scientist have been looking at the entire microbiome. They do this using something called high-throughput genetic sequencing of the 16S ribosomal DNA sequence. The researchers who published this study were from the University of British Columbia in Vancouver, and investigated the microbiome of 319 babies at both the 3 month and at the 1 year mark. They then tracked the health of these babies over 5 years (where they looked at overall health at the 1 year/3 year/5 year time points).

Researchers found a significant difference in 4 key populations of bacteria. Children who were low or missing these four types of bacteria had a much higher chance to go on to develop asthma as they aged. The key missing bacteria were from the genera Lachnospira, Veillonella, Faecalibacterium, and Rothia. 

First of all let me stress: These are NOT bacteria that come from eating yogurt or taking probiotics. These are specific bacteria found in the normal guts of newborn infants and were only found using this new method of sequencing ALL the bacteria found in the gut. It is important to note that only these new techniques allow us to see and compare all the bacteria in the gut  (it is be very hard to culture or identify even a fraction of the normal microbiome using the old standard techniques for bacterial identification).

But to prove it was the loss of these missing organisms that were CAUSING the problem, mice grown in a germ free environment were given microbiota from babies in the study lacking these four kinds of bacteria. The mice given this type of flora developed inflamed lungs similar to what is seen in asthma.

When they reconstituted the mice with microbiota containing high levels of the four key genera of bacteria, mice were no longer at risk for developing asthma!!!

The scientists in the study were also looking for commonalities in the babies that were missing the important microflora. Were they delivered by C section? Were they given more antibiotics? Were they breast-fed or given formula? Did they live in the city or on a farm. This study indicated that the only factor that seemed to predict the loss of these important four types of bacteria was early exposure to antibiotics.

They are going to continue look to determine if the identification of missing specific organisms in the microbiota of newborns could be an early detection system for allergy and asthma in the future. Also, they are looking to determine if reconstitution of the missing bacteria could be protective!

Stay tuned for more!!!


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In my previous blog post, I was discussing how Consumer Reports had conducted an investigation into contamination of retail chicken with known bacterial pathogens. We then discussed in class ground beef, and the likelihood that it will always be contaminated with bacteria. Consumer Reports came through for me again, and in their report: How safe is your ground beef?, they essentially proved me correct. Most ground beef, simply by the way it is processed, would generally be exposed to colicoliform bacteria (bacteria found in poop). What they found was all samples tested contained these bacteria.

And before we go any further,  let me stress, that thoroughly cooked hamburger is completely safe. Once your food is cooked (this means inner temp of your burger) is at 160 degrees F, the bacteria that are there are dead. Dead bacteria cannot hurt you. However, if your burger is pink inside, the bacteria that are there are still viable.

What kinds of bacteria did they find? They tested 300 samples of ground beef from various sources- big box stores, whole food stores (conventionally raised cattle, and those from sustainably raised cattle) . They tested for the five main types of bacteria that are indicated in disease from contaminated food: Various strains of E. coli (including O157),  Clostridium perfringens, Staphylococcus aureus, Salmonella, and Enterococcus.

20% contaminated with C. perfringens
10% with S. aureus- strains that included food superantigens

But worse yet, 18% ground beef from conventionally raised cattle were contaminated with superbugs (bacteria resistant to three or more antibiotics). Ground beef from sustainably raised  cattle had 9% contamination from superbugs.

More about this tomorrow….

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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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