The End

It's the end of of a long but fruitful semester Unfortunately, I probably won't be posting any longer. I hope this blog shared some useful information. It was fun reading about all the current (and not so current) events and research taking place right now. Soon I hope to use this knowledge to help others get well and prevent the spread of infectious diseases. For now, thanks for reading and goodbye!

Using Viruses Against Resistant Bacteria

   by  AJC1 

Bacteriophages (phages for short) are viruses that infect bacteria, usually only a certain species or strain. In the 1920s and 1930s phages were used to combat bacterial infections before the widespread use of antibiotics. The introduction of antibiotics pushed phage therapy out of use because phages were difficult to study and manipulate and antibiotics were easier to administer and could cure numerous infections. Phage therapy is still being used in some countries in the Baltic and Eastern Europe. Modern medicine has seen vast improvements in molecular biology, genetics, and biochemistry that could make bacteriophages the successor to antibiotics and a cure for antibiotic-resistant infections.

Bacteriophages are highly specific and can be modified to only infect a pathogenic microbe. Phages by nature only attack bacteria and can be safely administered to other organisms, including humans and livestock, with very little risk. There are no side effects and the body naturally eliminates the phages.  Antibiotics are chemicals designed to damage and destroy bacteria unrestrained, whether or not the affected microbes are virulent or normal body flora. The destruction of beneficial bacteria can lead to further infections by opportunistic pathogenic bacteria and could upset homeostasis. Phages are specifically modified to target a single microbe and can be selected to only attack one strain, so virulent forms of common beneficial bacteria can be eliminated without killing normal body flora.

Bacteriophages are better on-site antimicrobial agent compared to oral or injected antibiotics. Chemicals released into the body are absorbed, spread, and eliminated. The site of an infection (inflamed wound, lymph nodes, organ, etc.) might only get a diluted compound that may not be effective. One of the reasons antibiotics are prescribed for several days to weeks is to build up a concentration that is lethal to the pathogens. Missing a dose could lower the concentration in the body and allow resistant bacteria to survive.  Parts of the body that have nothing to do with the infection also get a lethal dose and normal bacteria die. A bacteriophage grows in the target bacteria, so it concentrates where the target is concentrated. The infected area quickly becomes saturated with the virus as it infects bacteria, multiplies, lyses the cell, and attacks other targets nearby. It is an exponential growth of the virus where it is needed most, and causes the pathogen numbers to exponentially decrease. The virus is not active where targets are not present and does no harm except to the specific species or strain for which it is designed for.

Bacteriophages can be modified to enhance their specificity and prolong their effectiveness. Genetic engineering and molecular biology have made it possible to alter viruses to make them more potent and more specific. A virus or family of viruses could be altered several times to attack bacterial species within the same genus. The benefits are “custom” treatments that will target only the microbes that are causing a disease.  Bacteria can eventually develop some immunity to a virus. 

To make treatments effective, it is usually necessary to combine several viruses into a cocktail that targets one to several species in several different ways. It makes it harder for bacteria to react and become resistant, and even kills already resistant strains because multiple different phages are present. Over time, it will probably be necessary to modify the virus as bacteria start to cope with it, and in some instances phase out phages that are ineffective. However, it is not known how many times a virus can be altered, and there are hundreds of bacteriophages to use. Once the knowledge and technology are established, it would be very easy and relatively inexpensive to quickly change the cocktail, and it could be changed many, many times.

A few problems with phages are present right now. The technology and research are not at a commercial state yet, so engineering viruses is still expensive. The viruses need to be in a cocktail of several types and an adjunct to make sure the virus stays in the body long enough to kill all the target cells. The easiest and least expensive way to culture large amounts of virus now is to grow host bacteria and let the virus replicate in the host. Certain highly specific bacteriophages to highly virulent species have to be grown in the cell, which means facilities growing large quantities of dangerous organisms. Phages are made primarily from proteins, so there is a risk that it will be viewed as an antigen and could illicit an immune response such as an allergic reaction. But there is another benefit viruses can have without actually using live phages.

Bacteriophages produce a class of enzymes called lysins that digest the cell wall of bacteria and kill the cell.  Lysins are used by the virus the break down the cell wall prior to bursting the cell and releasing copies. They can lyse cells from the outside as well, even when phages are not present.  The enzymes have been isolated and research is being done to find uses for it. Lysins could be administered just like antibiotics, but they are more specific. Some lysins will only kill one species of bacteria but will not harm other species from the same genus. There are many lysins already available, and there is no indication that bacteria can build a resistance to it.

Phage Renaissance 

Antimicrobial Nanoparticles and MRSA

   by  EMSL "Zinc Oxide Particles"

A study done last year shows that certain nanoparticles can kill bacteria, even MRSA and other resistant strains. The nanoparticles are made with zinc oxide (ZnO) and titanium dioxide (TiO2). The researchers believe one of the ways these resistant species are so hard to control is their ability to form biofilms. Biofilms are large aggregates of bacteria that produce a matrix. The matrix protects some of the bacteria by not allowing antibiotics to come in to contact with the bacterial cells. The study focuses on the effectiveness of nanoparticles on the bacterial biofilms of MRSA.

Several isolates of MRSA that were shown to produce biofilms were cultured and allowed to aggregate. Commercially produced TiO2 and ZnO nanoparticles were introduced and the effects were measured. The particles had much greater inhibitory effects than all the antibiotics tested with it. Even low doses were better than most antibiotics, and some doses even prevented biofilms from forming. The results show that nanoparticles can be valuable tools to combat resistant bacterial strains. Using the particles to coat medical devices where biofilms readily form, like catheters, may prevent the formation of biofilms. Other possibilities for drugs or use with antibiotics should be researched further.

Antimicrobial Activity of Zinc and Titanium Nanoparticles against Biofilm Producing MRSA

Ants and Disease Transmission

   by  tarotastic 

Entomology and Biology professor David Hughes from Penn State was given the lead to find out if ants can teach us about the spread of disease in certain environments, such as large communal groups and offices. The National Science Foundation and the National Institutes of Health granted Dr. Hughes and his team a $1.8 million grant under the Ecology and Evolution of Infectious Diseases research initiative. The initiative "supports efforts to understand the underlying ecological and biological mechanisms that govern relationships between human-induced environmental changes and the emergence and transmission of infectious diseases."

The researchers will introduce various agents to ants and track the transmission. By varying the colony size and complexity, they hope to produce a mathematical model to expain the spread of diseases in populations that can eventually be used to predict transmission routes of human pathogens and help manage outbreaks. The team believes that ants can provide a reliable interactive community which to base the model on. Ants can be manipulated and colony size and structure can easily be changed to fit the goals of the researchers, and they're behavior is similar to other social groups.

A positive side effect of the study is an in-depth look at ant colony interactions. The social structures and methods of carrying out tasks could lead to a better understanding of how colonies react to insecticides that could be used to create more effective means of controlling pest ant species. The mathematical model of transmission could also be applied to livestock and agricultural diseases, leading to better prevention strategies and healthier animals and crops.

Penn State Study
Ecology and Evolution of Infectious Diseases Initiative

Infections From Cats

This weekend some friends finally got me to watch the BBC show "Sherlock". I know it's in its 3rd season, but I'm usually behind on things like this. Anyways, I've made my way through the 1st season, and its pretty good, even if some of the lab tests he performs are wrong or impossible, but that's another topic. In the 3rd (or last) episode, a woman dies from what seems to be an infection, but they are unable to figure out how she was infected. Watson visits her home and believes it was cat scratch. I'm not going to give away any more, but this got me thinking about cats. My family has had our share of cats, and along with that cat scratches. So what are some things you can get from your overly playful cat?

Cat scratch fever (Bartonellosis) is a bacterial infection caused by Bartonella henselae. It is the most common bacterial disease acquired from cats. The bacteria are commonly found in cats and don't usually cause a disease until it enters into the bloodstream. Fleas can also transmit the bacteria. Kittens are the most prone to harboring the bacteria and causing an infection in people or spreading it to other cats. Cats can also carry Salmonella and can infect through a scratch.

Cats may also have dirt in the claws, which can have a lot of bacteria found in soil that are pathogenic. The genus Clostridium lives in the soil and can cause tetanus and botulism. Bacillus can cause serious infections, including anthrax. Listeria and Camplybactor may be found and can also be transmitted via cat scratches.

This is not a comprehensive list, but just some common infections that can be passed from cats to humans.

Cornell Veterinary College
Soil-Related Bacterial Infections

UPDATE: Chikungunya Virus

Over the last week four more cases of Chikungunya virus have been reported in Alabama, along with the Huntsville case last week. One of those cases was in Birmingham. So far, all the people infected were travelers to parts of the Caribbean and no cases of infection from Alabama mosquitoes have been reported. However, the disease can cause relatively mild symptoms that may seem like allergies and a bad week of arthritis, which may prompt some people to stay at home instead of going to the doctor, so the exact number of actual cases is unknown.

There is still worry that the virus will spread to mosquitoes in the Southeast and an outbreak will occur. The CDC recommends following mosquito bite prevention guidelines, which can be found on their website and in the previous post. The CDC also urges anyone who has a fever and joint pain to see a doctor. There is no treatment and symptoms go away in about a week, but it is important that clinicians correctly identify cases of the virus so the infection patterns and numbers can be used to gather information and monitor its spread.

Certain Caribbean regions have been assigned Precaution Level 1 because of Chikungunya virus outbreaks. Anyone traveling to the Caribbean or South America should look up the region on the CDC Traveler's Page, which has information on current outbreaks and how to best prepare for travel to those regions.

CDC Mosquito Bite Prevention Guidelines

• Use air conditioning or window/door screens to keep mosquitoes outside. If you are not able to protect yourself from mosquitoes inside your home or hotel, sleep under a mosquito bed net.
• Help reduce the number of mosquitoes outside your home or hotel room by emptying standing water from containers such as flowerpots or buckets.
• When weather permits, wear long-sleeved shirts and long pants.
• Use insect repellents.
• Repellents containing DEET, picaridin, IR3535, and oil of lemon eucalyptus and para-menthane-diol products provide long lasting protection.
• If you use both sunscreen and insect repellent, apply the sunscreen first and then the repellent. 
• Do not spray repellent on the skin under your clothing.
• Treat clothing with permethrin or purchase permethrin-treated clothing.
• Always follow the label instructions when using insect repellent or sunscreen.

AL.com 4 More Virus Cases
CDC Chikungunya Virus
CDC Traveler's Page

Chikungunya Virus in the Southeast

The virus is transmitted by the yellow fever mosquito, which also carries yellow fever and dengue fever. The virus can cause fever and joint pain that can be debilitating in severe cases. The virus cannot be transmitted between people, but only by mosquito bite. There is no vaccine against it. Chikungunya outbreaks have been reported in several Central American and Caribbean countries in the past two years. So far, all the reported cases in the U.S. have been by travelers to countries where the virus is established.

The virus can spread by a mosquito biting someone infected and then biting someone without the disease. The CDC is worried that the virus will spread to the United States from either infected mosquitoes from Caribbean countries or from infected individuals introducing the virus into the yellow fever mosquitoes already found in the United States, and possibly other mosquito species.

Symptoms develop within 3 to 7 days of infection. The fever usually lasts a few days to a week, but the joint pain may last more than a month. Anyone with a fever, headache, rash, and/or joint pain should go to a doctor.

The CDC gives guidelines to prevent mosquito bites and possible infection.

• Use air conditioning or window/door screens to keep mosquitoes outside. If you are not able to protect yourself from mosquitoes inside your home or hotel, sleep under a mosquito bed net.
• Help reduce the number of mosquitoes outside your home or hotel room by emptying standing water from containers such as flowerpots or buckets.
• When weather permits, wear long-sleeved shirts and long pants.
• Use insect repellents.
• Repellents containing DEET, picaridin, IR3535, and oil of lemon eucalyptus and para-menthane-diol products provide long lasting protection.
• If you use both sunscreen and insect repellent, apply the sunscreen first and then the repellent. 
• Do not spray repellent on the skin under your clothing.
• Treat clothing with permethrin or purchase permethrin-treated clothing.
• Always follow the label instructions when using insect repellent or sunscreen.

CDC Chikungunya virus
 AL.com First Alabama Virus Case

Yersinia Infections in Transfusions

  by  makelessnoise 

Yersinia enterocolitica is a human pathogen that affects the G.I. system. It causes fever, diarrhea, and abdominal pains, and can sometimes be mistaken for appendicitis and is usually spread by contact with fecal material. However, it is a very important infection in blood banking, as it is the leading cause of post-transfusion septic infections.

Y. enterocolitica is a common contaminant is stored blood. The bacteria has several adaptions that allow it to thrive under the conditions blood is stored. Yersinia species are siderophilic, meaning they like high-iron environments, as is in stored blood. Y. enterocolitica can survive and even reproduce in temperatures down to -2C, allowing them to grow at the refrigerated temperatures blood is stored. The bacteria use glucose and adenine, found in storage additives, for metabolism and growth, and have an optimal pH of 7.0 – 8.0, and blood is stored around 7.3. It has been shown calcium prevents growth of pathogenic Yersinia but only above 30C, so blood stored with a calcium chelated anticoagulant does not prevent infection.

Y. enterocolitica can cause an asymptomatic infection in the intestines that disseminates to the blood, which is how is eventually contaminates stored blood. Donors who are asymptomatic or who have bacterial counts low enough to not present symptoms are not routinely screened. The bacteria do not actively cause sepsis, but trigger a major generalized inflammatory response, thought to be the result of a cell wall component that strongly binds to and activates macrophages, who initiate a cytokine cascade throughout the body.

Serologic donor testing is expensive and infections caused by Y. enterocolitica is relatively rare. The simplest ways to prevent post-transfusion infections from the bacteria are not allowing donors the give blood if they do not feel well or have any signs of infection, not giving blood older than 3 weeks to susceptible recipients because the  bacteria take 3 to 4 weeks to reach dangerous levels in refrigerated blood, and using pre-storage leukocyte-reducing techniques because the bacteria have a strong affinity for WBCs.

http://www.ncbi.nlm.nih.gov/pubmed/21865196

Sous-vide Cooking and Bacteria

I have a confession: I love to cook. It's a combination of art and science, and you can eat the final product! My favorite aspect of cooking is food science and learning the processes that take raw ingredients and turn them into food, and I read a lot about modern and next gen cooking techniques. That's how I learned about and started using sous-vide.

  by  AustinMatherne 

Sous-vide is a cooking method like baking, broiling, or grilling. Food is placed into a vaccum-sealed bag and usually submersed in a water bath. The water is kept at a precise temperature using some type of heater/thermostat combination and the food is cooked by heat diffusion through the bag. The food cooked this way is not soggy, the flavors are sealed with the food, and extremely specific temperatures can be used. Most sous-vide is done with meat. Steaks can be cooked to a perfect medium-rare just by setting the temperature to the correct degree. And because the water, and therefore the food, never exceeds that temperature and no moisture is lost, food can be left in it for days without overcooking. The problem is most sous-vide cooking takes place between 120F to 150F; in the bacterial danger zone.

The theory behind preparing food safely is bacteria don't have a thermometer that kills them only if a certain temperature is reached. There are charts, graphs, and computer models that predict the death rate of certain food-borne pathogens, and the rate is a curve. Cooking chicken to 165F kills salmonella in a few seconds, but it take several minutes to completely kill at 150F. So theoretically, as long as you let food sit in the water bath long enough, it will pasteurize it and be as safe as conventional cooking, while being juicer and more tender.

However, most models for recommended cooking times do extend into the low temperatures that sous-vide uses. Many publications exist, but few actually link scientific or regulatory reports for the cooking times. Here is a page from a popular sous-vide immersion circulator company that lists times and temperatures, but the only source is a link to the FDA homepage. Most cooking times are based on the old models for high temperature, so the temperatures are not approved by food agencies. But the Institute of Food Research in the UK and the USDA/FDA have both begun programs to update the current models to include low temperature cooking.

I personally don't have a problem with sous-vide and have made several meals at home without any problems using the times provided from other chefs, as have many other people. I will continue to use sous-vide as an alternative cooking method and use safe food-handling practices when cooking to keep the risk for contamination low.

Douglas Baldwin: A Practical Guide to Sous Vide Cooking

Institute of Food Research Bacterial Growth Model Study pdf

Glowing Burn Dressings Detect Infections

Burns are some of the most difficult wounds to treat. Large open sores are easy for bacteria to colonize, and most serious burns require hospitalization, which can lead to exposure to infectious pathogens. The pathophysiologic response to a burn, as well as its involvement with skin that is colonized by opportunistic pathogens, are the major reasons for infections. A burn compromises the innate protection of the skin, decreases T-cell activity by decreasing the number of helper cells, decreases the levels of inflammatory cytokines and complements, and decreases the bactericidal activity of neutrophils. Common bacteria that infect burn wounds include Staphylococcus aureus, Pseudomonas aeruginosa,  Klebsiella pneumoniae, and Acinetobacter  baumannii.  

Currently, if an infection is suspected, the wound dressing is removed so a swab or scraping can be obtained. This exposes the wound, increases healing time and the likeliness a scar will develop. Testing of the sample can take several days to culture and identify the bacteria. The University of Bath's biochemistry department has developed a wound dressing patch that fluoresces in the presence of infectious bacteria. Most bacteria causing infections release toxins. These toxins break down nanocapsules which are filled with a fluorescent compound and bacteriophages. The fluorescent chemical glows under UV light, alerting doctors to an infection without removing the dressing, and can even detect toxins at concentrations below that which the body starts reacting, allowing doctors to start treatment before the bacteria cause an actual infection. The bacteriophages are viruses that attack and kill bacteria. They can help prevent and stop infections, even by those caused by microbes like MSRA that are resistant to antibiotics. The patches work well in the laboratory, but it will be some time before human trials begin.


University of Bath Research

Burn Wound Pathophysiology

What's Swimming in the Pool With You?

Over the last couple of weeks pools have been opening for the summer. I have a few friends with pools and live close to a large public pool. I know a lot of work goes into keeping the water as clean and clear as possible. Chlorine is a common additive to kill microbes and it does a pretty good job, but are there some out there that can survive? What kinds of bacteria are in public pools? How do I avoid getting an infection from something in the water? The CDC has the answers.

  by  Innisfree Hotels 

Swimmers

The CDC conducted a study of swimming pools in 2012. They sampled water filters in public pools to see what was potentially in the water. They found Escherichia coli in 58% of filters they tested. This indicates a lot of fecal matter enters the water. E. coli is common in the human gut and in feces, so it's presence in water is a marker for fecal contamination. People contaminate pools with feces when they have an "accident" in the pool or it washes off the body from people who haven't showered before entering the pool. On the bright side, no samples tested positive for O157:H7, a particularly virulent strain that produces a deadly toxin.

The CDC also found Pseudomonas aeruginosa in 59% of samples. P. aeruginosa is a bacteria that causes skin rashes and ear infections, and is the bacteria behind "Swimmer's ear". It is a natural contaminant, usually from inadequate chlorine and pH levels, and is also introduced from people. Cryptosporidium and Giardia were found in less than 2% of samples. Cryptosporidium is a bacteria that causes a bowel disease similar to dysentery. Giardia is a parasitic protozoan that causes diarrhea, vomiting, cramps, and dehydration. The study did not test water parks or residential pools, but believe the hygiene, sanitation, and contamination between pools is similar due to the most common microbes coming from swimmers themselves.

Prevention

The CDC recommends swimmers: 
Keep feces and other contaminants out of the water.
  -Do not swim when you have diarrhea.
  -Shower with soap before you start swimming.
  -Take a rinse shower before you get back into the water.
  -Take bathroom breaks every 60 minutes.
  -Wash your hands with soap after using the toilet or changing diapers.
Check the chlorine level and pH before getting into the water. 
Do not swallow the water you swim in.

Happy swimming this summer!

CDC Study 
CDC Healthy Swimming 

Fungal Infections

The last couple of weeks we have learned of a few infectious fungi like Cryptococcus sp. and Candida sp. We study bacteria and bacteria-related infections in depth, but very time is spent on fungal infections. A lot of people, including me, think it weird that something like yeast can cause a serious infection. The stuff you make bread with can make you sick? No way.

We talk about yeast and species of fungi, but I still associate it with the powder I mix into dough to get it to rise and the stuff in beer and wine that makes alcohol. I wanted to find out more about diseases caused from fungi, and what I did find was interesting. I didn't know there were so many species that had nothing to do with the carbon dioxide-producing baking aides. Here are some of the highlights.

Fungal Infections and HIV/AIDS

Fungal infections aren't something that happens often, and that's because our body does a great job of stopping infections and killing invaders. Fungi generally aren't protected by much and take a much longer time to grow and establish themselves than a bacterial infection would. But in a patient who was a weak or non-functioning immune system, opportunistic infectious agents have an easy time colonizing the body. That's why most fungal infections are seen in immunocompromized patients and why they are so serious. According to the paper linked below, around 50% of AIDS-related deaths are caused by fungal infections. Here are some of the most common fungal infections in HIV/AIDS patients.

Cryptococcosis

  by  Pulmonary Pathology 

Cryptococcosis is caused by Cryptococcus neoformans. The fungus is inhaled and enters the lungs. The lack of protection from alveolar macrophages allows the fungus to spread to the blood, and later to the brain and CSF. Encephalomeningitis causes increased cranial pressure that leads to death. Sub-Sahara Africa sees the majority of infections, but the infection can occur in all populated areas. This is considered one of the more dangerous fungal infections because without help from the bodies' immune system it is difficult to clear and once symptoms appear the disease progresses rapidly. However, once the fungus is detected, the mortality rate for developed countries is about 9% but 70% in developing countries. Drugs like Amphotericin B and flucytosine are used in treatment. The defining identification of cryptococcal meningitis is a positive India ink stain of CSF fluid, but the fungus can be found in other tissues, especially the lung and brain.

To Be Continued

A neglected epidemic: fungal infections in HIV/AIDS.

Colleges Using Unapproved Meningitis Vaccines

Princeton University and the University of California Santa Barbara recently experienced outbreaks of meningitis B. Meningitis B is a serologic group of bacterial meningitis. Meningitis in general is highly contagious in close quarters, such as college classrooms and dorms. There are FDA approved vaccines for other serologic groups, but no vaccine for type B.

There are 8 reported cases at Princeton and 4 at UCSB. The first case at Princeton was found in March 2013 and the first case at UCSB was found in November 2013. With no vaccines, Princeton was worried about the infection spreading. They were allowed to use an unapproved vaccine by the FDA under an "Investigational New Drug" tag to use the vaccine Bexsero, which is the only vaccine to protect against type B. The vaccine is approved in Europe, Australia, and Canada. About 5,000 students were vaccinated. Later that year, type B meningitis infections were found at UCSB. The same vaccine was allowed to prevent further outbreaks. A booster shot was offered at Princeton in February.

The CDC reports the FDA claims the vaccines are safe for use in specific situations, such as outbreaks in susceptible populations. There are no major side effects except a severe allergic reaction, which is extremely rare. The FDA uses the IND tag to approve use of a drug they feel is safe and the benefits are greater than the risks, and they applied it to Bexsero because they have not yet approved it for use for the general public in the US. The vaccine is a two-part intramuscular shot that requires a second booster 6 months after the initial vaccination to maximize protection.

Huffington Post

The Princeton Sun

CDC Type B Vaccine and Outbreaks

Welcome

My name is Zack and I'm a Clinical Laboratory Sciences (CLS) graduate student. I'll be posting interesting things from Infectious Diseases and Microbiology classes or outside sources I find that relate to the courses. So for an intro, I'll answer a few common questions.

What is a Clinical Laboratory Scientist?

Well, to start off I think it's best to say what we are not. We are not nurses or doctors. We work very closely with them, but we are definitely a separate field.  CLS and Medical Technologists are specialists in the clinical lab. We handle samples like blood, tissue, and other body fluids and analyze them to find out more about patient health and disease states. We are most commonly found in hospital labs, but also work in reference labs, private offices, and government facilities.

What's the difference of Microbiology and Infectious Diseases?

Microbiology is the study of microscopic organisms such as bacteria, yeasts, and parasites. Microbiology is all about the classification and characterization of the organism. We learn how to classify and identify bacteria based on growth patterns, staining, biochemical tests, antimicrobial susceptibility, and even physical senses like color and smell. Micro focuses on the just the organism.

Infectious Diseases looks at the associated diseases caused by the organisms.  It is about classifying organisms based on common disease traits to help pinpoint the organism or group of organisms most likely responsible so the best treatment and therapy can be given to a patient.

I hope this gives you some idea what this blog will be about!