Author Archives: ycpmicro

Beware of the brain eating amoeba -Naegleria fowleri

Maria Allera (11 AM Micro) is worried about parasitic diseases, and with good reason. She found a news alert about the brain eating amoeba, which has long been one of my favorites. Who can forget this classic episode of House which featured Nagleria, and was one of the last times I got to trot out the #BOGUS hashtag? Let’s see if Maria can make us feel better about Nagleria:

Naegleria fowleri is an amoeba that takes residence in warm, fresh water all over the world. Just two weeks ago N. fowleri turned up in a water supply in Louisiana, causing the town to go into a state of emergency to provide bottled water for all the residents. N. fowleri can be found in any body of water, such as lakes, ponds, rivers and even manmade structures like pools or waterparks. The amoeba thrives in hot water and can also be found in water discharges from industrial plants.

When N. fowleri comes in contact with a human it makes its way into the body through the nasal passage, swims to the brain and causes an often fatal infection called Primary Amebic Meningoencephalistis (PAM). Some symptoms of PAM include headaches, fever, nausea, vomiting, hallucinations and coma; all of these can lead to death. Since the 1960’s only 200 conditions have been reported, unfortunately less than 5% survive. The infection can be diagnosed when examining spinal fluid under a microscope to identify the amoeba. Under the microscope the amoeba appears as:

Naegleria fowler is elongated, 15-30 μm, and feeds on Gram-negative bacteria. The cytoplasm is granular, has a single nucleus with a prominent and contains vacuoles. Blunt lobular pseudopodia are formed at the widest point. The flagellated form is smaller, with a pear shape and two flagellae at the broad end. N. fowleri cysts are round, 7-15 μm in diameter and have a thick smooth double wall. N. fowleri is thermophilic, preferring water temperatures between 35 and 46ºC (link here)

Within the amoebas life there are three stages. The first two stages, the cyst and flagellate stage, require low food supply and low temperature. When an amoeba is in the cyst or flagellate stage it cannot survive in human tissue. The human body is the perfect living condition for the trophozoite stage. The amoeba feeds off of the human blood cells, it reproduces by binary fission and destroys other tissues. As dangerous as this microorganism sounds, it all depends how it is ingested to determine if it will cause harm or not. If you consume water with N. fowleri in it, it will process through your digestive system without any health problems. This amoeba is only dangerous when it gains nasal access.

Naegleria fowleri in its trophozoite stage, from the CDC

Just like any pathogenic disease everyone wants to know how to prevent acquiring it and how to treat it if acquired. To prevent contracting N. fowleri, it is smart to not submerge your head in fresh water, especially if it is a warm temperature. Try to always swim in treated waters and don’t wash your nose out with fresh water. Do not use a neti pot to clean your sinuses, the water goes straight up the nose so if the water is effected you’re putting your body directly at risk. Unfortunately most infections of N. fowleri end in death, there are a few survival stories. There have been four survival cases in North America, a laboratory did testing and the CDC released

It has been suggested that the original U.S. survivor’s strain of Naegleria fowleri was less virulent, which contributed to the patient’s recovery. In laboratory experiments, the original U.S. survivor’s strain did not cause damage to cells as rapidly as other strains, suggesting that it is less virulent than strains recovered from other fatal infections.

Amphotericin B  was the most common medicine to treat amoebas. It’s inserted directly into the brain; however, this treatment usually fails. The CDC also has an investigational drug on study called Miltefosine for three free living amoebas including N. fowleri and it has had much better results.

Biofilm Basics and Treatment

Abby Nicodemus (11 AM Micro) found a news story via Scientific American, describing recent research published in the journal Proc. National Academy Sciences. The compounds described are being assessed for their antimicrobial properties. Because they are general inhibitors of microbial growth which operate by creating an environment unfavorable for growth, it is possible that this approach will not lead to antimicrobial resistance the way so many other compounds do. Here is Abby’s summary:

Biofilm growing on a grain of sand; image via Flickr

The focus of health care is to “[maintain] health by the treatment and prevention of disease especially by trained professionals”, so any scientific advance in the field of bacteria and disease has the opportunity to contribute to the health care field. While scanning through the current topics of microbiology, I stumbled upon an article titled “Liquid Salts Bypass Skin to Treat Infections” and it sparked my interest. Diseases and treatment of diseases being what we are studying in lecture, I thought it would make sense to discuss it in my bonus summary.

The first paragraph of this article discusses biofilms, “packed communities of microbial cells that grow on both living and inert surfaces” (Liquid Salts), which reminded me of the samples we took for the third lab. The significance of biofilms is the part they play in human infections, they are responsible for 4/5 of human infections. A large majority of microbiology focuses on human diseases and treatment. The source of infections and diseases is incredibly relevant in understanding and making scientific discoveries. Knowing more about these infections can help to lower hospital visits. It is known that biofilm infections are responsible for “almost one out of every ten visits” (Liquid Salts).

Specifically regarding biofilms, the structure of these bacterium increase their ability to fight off any treatment, including antibiotics. Skin, our protective barrier, does a more than okay job of keeping things outside of the body, making skin treatment options limited. However, innovations in science have made new categories of treatment a reality. This discovery involving salt absorption through skin widens the possibilities of fighting off infection.

Many of the ionic formulations brought forth by Mitragotri and his team showed effectiveness against treating many bacterial microfilm infections. This study has helped to tie a number of loose ends because “individual parts…have been demonstrated before, but this study draws them together in a very coherent strategy”. Ideas have been proposed involving this method, but only recently have discoveries given those ideas significance and the reality to help the millions of people affected by these diseases.

This technique decreases the amount of bacteria in the body by almost completely eliminating biofilms and minimizing the release of toxins into the human body. Currently, only specific ionic salts have been discovered and engineered to fight infection, but more research can lead to a broader spectrum of treatments for a wider range of infections. Certain salts and ions will penetrate the skin and target certain biofilms more efficiently than others.

Advances are being made in the medical field every day, but this particular discovery has the potential to change the world of disease and help many more people who suffer from bacterial infections and diseases. By eliminating biofilm infections, we can reduce the amount of money spent on treatments and the number of people admitted to hospitals for these kinds of infections will also go down.

Notes from the Field: Expired Influenza Vaccines

In what will undoubtedly be ammo for the antivaxxer movement, the latest issue of Morbidity Mortality Weekly Report from the CDC reports the ongoing surveillance of vaccine administration for seasonal influenza is not perfect. The seasonal influenza vaccine comes in two forms: an inactivated virus formulation that is injected, and a live, attenuated virus formulation that is administered nasally. Both forms of the vaccines are generally widely available in late summer/early fall, and are recommended for the general population of the US for everyone over the age of 6 months. The inactivated vaccine has an expiration date of June of the following year, and is contraindicated for use at that time, mainly because of the lack of protection that it will offer to novel influenza strains that will have arisen by that point. The live attenuated vaccine on the other hand has an expiration date of about 18 weeks (4.5 months), and should be disposed of at that point even if the flu season is still going on. Since the flu season generally runs from November through March, it generally should not expire during this time, however if the vaccine is produced but not administered earlier in the season, stockpiles of expired vaccine may accumulate.

Epidemiologists from the CDC analyzed data from the national Vaccine Adverse Event Reporting System (VAERS), from 2007 through 2014. Of reports using live virus vaccines, approximately 18% of those reports indicated that expired vaccine had been administered to patients, and the vast majority of those reports did not document any adverse health events. The most likely outcome due to administration of any expired vaccine is a lack of protection against season flu. Consequently, revaccination with a valid dose is recommended to maintain protection against flu. The CDC recommends that all health care providers be aware of the significantly shorter shelf life of the live vaccine, and to be aware of return and replacement options from vaccine manufacturers.

Measles, now at epidemic levels

I saw this story at, which summarized a news alert from the Centers for Disease Control about the ongoing outbreak of measles in the US. In the year 2000, measles was determined to essentially eliminated in this country, following an aggressive vaccination campaign during the second half of the 20th century. Prior to the introduction of the vaccine, there were over 500,000 cases each year, with a death rate of about one per 1000 cases. Because of the perceived low rate of death due to measles, there is a public perception that it is not a very serious disease, however there is actually a high risk of complications from measles that can lead to extensive medical care. Up to 30% of measles cases have one or more complications, with pneumonia being the most frequent cause of death in children due to complications of measles. In countries where malnutrition is prevalent, death due to measles occurs in 25% of the cases.

The graphic above was published by the CDC this week, and documents the rise in measles cases over the past decade+ since the disease was declared “eliminated” in 2000. This year marks the highest number of cases in over 20 years, and this milepost has been reached by the end of August, not the end of the calendar year. The CDC attributes the spike in cases solely on failure of parents to vaccinate their children; essentially all of the cases in this year’s outbreaks have been in unvaccinated individuals. In the majority of the cases this year, a cluster of cases were observed–an outbreak–where a single patient infected unvaccinated people around them, resulting in many cases of the disease.

The CDC strongly recommends that all individuals be immune to measles through vaccination. Because of the high threat of complications, the added cost to society through lost wages and healthcare, and the highly contagious nature of the disease, it is important to not become complacent about its threats. Additionally, certain segments of the US population (the very young, others with specific sets of underlying medical conditions) are not immune to measles, and therefore are significantly at risk due to exposure by others. The United States along with other partners in the World Health Organization have pledged to eliminate this disease for good by 2020. If we all do our part, we can see this happen!

Fuel from E. coli

Figure 1: Enzymatic synthesis of propane

Figure 1: Enzymatic synthesis of propane

Via @AnP_prof and NBC News, this is a cool story about an advance in molecular engineering of E. coli to enable this bacterium to produce propane. The news alert points to a publication in the journal Nature Communications, describing research from scientists from the University of Turku in Finland, and University College London. I’ve talked about work using microbes to make fuels in several capacities (see here, here, here, and here for some examples), and the primary challenge is to enable it to be a process that is sufficiently efficient to make it worthwhile from an energetic, and a financial standpoint.

The main issue with using bacteria to make hydrocarbon-based fuel is that they are both very hydrophobic, and as a result are toxic to cells. Forcing a cell to produce these compounds then can create a situation where the cell is essentially poisoning itself. Additionally, other attempts to engineer biosynthetic pathways for fuel production generate products that require some amount of additional purification before use, which means additional financial expense and energy expenditure prior to having a usable product. The current research, although it is in the preliminary stages and currently only has generated small amounts of propane, has regardless produced fuel that can be used in an engine essentially immediately.

The scientists took advantage of an existing pathway in E. coli that synthesizes membranes–the hydrophobic barrier that surrounds all cells–and interrupted it. Membrane precursors were shuttled into an alternative pathway that produced propane in just a few steps. To accomplish this, they introduced specific genes from at least 5 other bacterial species into E. coli, in order to construct the biochemical pathway for the synthesis of propane. The novelty of the approach is that no pathway to generate propane had been identified in any prokaryotic species. The scientists propose at the conclusion of their study several approaches for optimizing the process in order to scale it up for industrial production. One direction they suggest is to transfer the synthetic pathway into a photosynthetic microorganism, which naturally accumulates many of the additional enzyme substrates (NADPH and reduced ferredoxin) in the pathway from the figure.

There are several advantages for propane as a terminal product; it makes up the bulk of liquid petroleum gas, which is extensively used in cars, home heating systems, and elsewhere, and propane easily switches between a liquid and a gaseous state at ambient conditions. This latter property means that it can be easily removed from a culture vessel, diminishing the toxic effects that it would have on the cells that produce it. Once it has been released and collected, it can then be easily returned to a liquid state, which facilitates storage and transport. The group anticipates that with successful scale up, this process may produce fuel for vehicles within the next 5 to 10 years.


Food allergies and our normal microorganisms

Peanuts_with_skinA news article that made the rounds through the popular press this week caught my eye: “Commensal bacteria protect against food allergen sensitization,” which appears in the early access section of the journal of the National Academy of Sciences. I have been a big fan of this type of research for a while now. The basic premise is this: our modern lifestyle has potentially begun to diminish the numbers and variety of microorganisms that live on our bodies in the absence of disease (the normal microbiota), and as a consequence, benefits that these benign organisms can confer to us are being lost. So far, loss of diversity of the normal microbiota have been correlated with a long list of ailments including potentially autism and cancer.

An opinion piece in this week’s Nature warns against drawing too many conclusions from these studies, and suggests that over reporting of some of them by the press reinforces the need to ensure that the public understand the distinction between “correlation” and “causation”–these concepts are frequently confused, and the distinction is sometimes not clear. Indeed, the editorial in Nature suggests that reporting of microbiome analysis and human disease should be tempered by asking 5 questions:

  • Can experiments detect differences that matter? Characterization of microbiomes is generally accomplished by sequencing very highly related genes, and this analysis may hide real differences.
  • Does the study show causation or just correlation? Many of the cases of a disease association with certain microorganisms may be the result of conditions in the body becoming favorable for the microbe, meaning the disease caused the microbes to alter.
  • What is the mechanism? Demonstrating causation is important, however without an explanation of how a change occurs, it is not sufficient.
  • How much do experiments reflect reality? Many of the putative effects of the microbiome on health involve germ free mice; that is mice that have been raised to have no normal microorganisms of their own, as this makes interpreting the effects somewhat easier. However, mice and humans are not the same, and the microorganisms that live on each are not the same.
  • Could anything else explain the results? Many things can cause disease, and other factors should be considered and tested.

With this in mind, I read the article on food allergies linked up at the top. The authors carried out the study to address the hypothesis that the normal microbiota of the gastrointestinal tract are able to guide adaptive immunity at this site. The intestinal tract of animals hosts an incredible variety of organisms in the absence of disease. The immune system needs to be non-responsive to these organisms, as well as to all of the food antigens that enter the digestive tract. Immune cells in lymphoid tissue along the digestive tract modulate signals between the microbiota and the epithelial barrier of the digestive tract, which helps to prevent an ongoing inflammatory response, and thereby promote a homeostatic relationship between the microbiota and the host.

The researchers first experiment was to treat neonatal wild-type mice with an antibiotic regimen prior to weaning to eliminate intestinal microbiota, then sensitized by gastric administration of Peanut Antigen (PN). Three weeks later, the mice were challenged with the antigen and allergic responses were measured a day later by collecting blood. Control mice had essentially undetectable levels of allergic responses, while antibiotic treated mice showed highly elevated levels of IgE. Analysis of the bacteria from feces of mice at the same time intervals also showed that the antibiotic treated mice had lowered levels of fecal bacteria, and greatly diminished diversity of fecal bacteria. Specifically, members of the prokayotic phyla Bacteriodetes and Firmicutes, present under normal conditions, were essentially absent in the antibiotic treated mice. These bacteria were replaced with members of Lactobacilli, a result consistent with another recent report examining changes in the microbiota of antibiotic fed mice. The results outlined above were achieved using outbred mice strains housed in pathogen-free, but not germ free conditions; therefore this study addresses one of the critiques above with the use of outbred mice.

This paper was also significant, in that the authors also propose a mechanism for how the immune modulation occurs. Recolonization of antibiotic fed mice with a group of Firmucutes from genus Clostridium (the major genus of the Firmucutes from normal mice), prevented the allergic response produced by peanuts. Dissection of the intestines from these animals indicated that specific T cells involved in adaptive immune regulation are more prevalent in Clostridia colonized mice. Additionally, mice colonized with Clostridia in comparison to germ free mice and control mice exhibited high levels of an immune cytokine Interleukin 22 (IL-22). The authors propose that IL-22 (induced by the presence of Clostridia) causes the intestinal epithelial barrier to be reinforced, reducing the permeability to dietary proteins. To address this possibility, they then measured the levels of food allergens in the bloodstream after intragastric gavage. Colonization by Clostridia resulted in significantly lower levels of these allergens in comparison to germ free mice, supporting this hypothesis.

The major conclusions of this paper support the important role of the benign normal microbiota in promoting health. Their model argues that tolerance to food antigens is aided by the presence of those antigens along with specific components of the normal microbiota. To translate this work to human therapies, the role of Clostridia needs to be confirmed in humans. Indeed, other work has shown that Clostridia species isolated from human feces do induce the same immune regulatory cells discussed above when transferred to germ free mice, suggesting that they may be playing similar roles in both species.


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