Press Announcements > FDA takes significant steps to address antimicrobial resistance

December 11, 2013 Leave a comment

Press Announcements > FDA takes significant steps to address antimicrobial resistance.

 

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Categories: The List

Nobel winner declares boycott of top science journals | Science | The Guardian

December 10, 2013 Leave a comment
Categories: The List

Prokaryotic pow-wows and tackling antibiotic resistance

August 13, 2013 Leave a comment

Drug development cost: ForbesAntibiotic resistance is and will continue to be a key issue in the years to come. Many pathogens have been dubbed “super-bugs” as a result of their ability to persist in the presence of multiple antibiotics. Some bacterial pathogens, like totally drug-resistant tuberculosis, MRSA, Klebsiella pneumoniae, and Acinetobacter baumannii are of particular interest because of their clinical prevalence and ability to quickly acquire drug resistance.

One primary concern with antibiotic resistance is the lack of new drug development. The median cost of developing a new drug is $4.2 billion dollars (forbes article), and without proper antibiotic stewardship, a drug may only be useful for 2 or 3 years. That’s not much return on investment. Big pharmaceuticals will not dump money into a drug without the prospect of long term revenue.

However, there are novel ways to tackle the issue of antibiotic resistance without the billion bucks. The most heavily researched mechanism of antibiotic resistance is mediated by a class of enzymes called betalactamases. 80% of the research in the field of antibiotic resistance has been focused on betalactams, and we seem to have forgotten that there are several other classes of antibiotics that we can play with. I discussed the problem of such heavy focus on one antibiotic here: Gripes with antibiotic resistance research.

Bacteria have gained resistance to every class of antibiotics including aminoglycosides, tetracyclines, quinolones, and polymyxins. Each method of resistance is typically granted by an enzyme, and these enzymes should be new drug targets. If we can inhibit an enzyme that grants resistance, then by coupling the new drug with an old antibiotic, we can reutilize obsolete antibiotics.

Another method that has recently gained traction is the inhibition of virulence factors. Most bacteria are not virulent, and incapable of infecting humans. Remember, the human body is an incredibly harsh environment for a microbe. However, those that are virulent typically carry genetic determinants that give them the ability to colonize a host. For example, Escherichia coli is a commensal bacteria of the human gut, but some strains have gained the ability to produce toxins or adhere to particular mucosal surfaces, making these strains virulent. The development of new drugs to inhibit virulence may be able to prevent disease. I briefly described one such method in Dealing with antibiotic resistance through anti-virulence factors, where inhibition of a toxin leads to survival of mice and protection from disease.

One process that can be considered a virulence factor is quorum sensing, a mechanism for bacteria to detect population density. Bacteria excrete peptides that they also have receptors for, and when the concentration of bacteria increases, so too does the excreted peptides. When the population reaches a particular concentration, gene expression changes and may induce virulence factors. Pseudomonas aeruginosa and A. baumannii are opportunistic human pathogens, and through quorum sensing are able to coordinate the formation of biofilms, a virulence trait. Inhibition of the quorum sensing may inhibit the progression of disease, and a method for discovering drugs that can inhibit this system is described in this paper published this month in PNAS: A high-throughput screen for quorum-sensing inhibitors that target acyl-homoserine lactone synthases.

The growing issue of antibiotic resistance is critical to global health, but the problem is still just a pea under a mattress and not enough attention has turned its way. Translational research and drug development are absolutely integral to advancements in the biomedical sciences, but basic research will give insight to novel drug targets and molecular mechanisms that we can utilize to cure disease.  The pre-antibiotic era and the days where a common strep-throat or UTI would kill you are gone. However, without progress in research, stewardship, and activism, we could certainly regress.

The unfounded fears of Influenza research

August 10, 2013 Leave a comment

Tweety has the fluAs if the H5N1 transmission papers weren’t talked about enough, now the likelihood of similar research with H7N9 has lead to more unfounded fears. The first report of a possible human to human transmission of H7N9 came out a few days ago, and rather than instill fear that scientists will “create a deadly virus just to prove they can,” this possibility of an epidemic should highlight the importance of studying such a pathogen.

This has been harped on by every scientist I know, but it apparently still needs to be said. Even if we tried to engineer a more virulent and transmissible virus, we would never be able to out-craft nature. Natural selection will take place, and an animal-to-human or human-to-human transmissible virus will eventually pass into humans, and it is our job to get ahead of it and find out where it is going. There isn’t a single pathogen we could engineer that nature wouldn’t be able to do better.

Maybe more importantly, nature does not stop playing the game even if we decide to quit. It is Jumanji, and we are the kids playing the game. Even if we want to leave all the horrors of the game behind, we can’t. We are but pawns in nature’s game of chess.

The value of understanding mechanisms behind a potential pandemic virus is immeasurable. In the highly possible scenario, where a few thousand people come down with serious illness caused by influenza H7N9, the worst possible thing we could say is “well you’re screwed because we stopped looking for a cure.” Even in the most extreme circumstance, where a lab strain is somehow released that is highly transmissible and virulent, the best way to combat the threat is to do more research. 

Biosecurity is something every lab takes very seriously. As researchers, we take precautions to prevent both samples from getting contaminated, as well as ourselves from getting infected. Scientists are humans, too. We would rather not get seriously ill, and thus we have measures to prevent exposure to pathogens.

The fear mongering will never end because layman-shocking sensationalized headlines sell. But like all trolls, they get off on your attention. So give them none, and leave the scientists and the ferrets to save your lives. After all, “it is a curious feature of our existence that we come from a planet that is very good at promoting life but even better at extinguishing it.” – Bill Bryson in A Short History of Nearly Everything.

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What happens under your skin when a mosquito bites

August 7, 2013 Leave a comment

Although mosquito tongues are analogous to needles, they are actually mobile and flexible structures. After puncturing the skin, the tongue searches for a blood vessel to feast on. Here’s what happens when a mosquito bites you:

Also fascinating is:

“When the mosquitoes were infected with the Plasmodium parasites that cause malaria, they spent more time probing around for blood vessels. It’s not clear why—the parasites could be controlling the insect’s nervous system or changing the activity of genes in its mouthparts. Either way, the infected mosquitoes give up much less readily in their search for blood, which presumably increases the odds that the parasites will enter a new host.”

It’s also possible that the mosquito’s tongue mobility or sucking ability is hindered when colonized by Plasmodium, causing the mosquito to spend a longer time searching for blood vessels, and increasing the probability of a Plasmodium to leave the mosquito and enter a new host. Maybe Yellow Fever and Dengue elicit a similar response?

Full article from natgeo here:

Here’s what happens inside you when a mosquito bites

Coughing is commonly not from the common cold

August 5, 2013 Leave a comment

A leading cause of respiratory disease in children is Respiratory Syncytial Virus (RSV), producing over 3 million cases of lower respiratory illness and about 100,000 deaths annually (Nair et al. 2010). RSV is classified as a virus in the family Paramyxoviridae, which are all non-segmented negative sense RNA viruses. Other viruses that utilize this method of replication include Mumps virus, Human Metapneumovirus (hMPV), and  Henipavirus, the inspiration of the movie Contagion. Like most viruses that cause respiratory symptoms, including viruses that cause common cold, numbers of RSV infections increase in winter months when people spend more time indoors (Florida is weird).

MMWR RSV 2007

Nearly all children will encounter RSV, but only 2-3% will require hospitalization. However, the real trouble is re-infection. Typically after your immune system develops antibodies against an antigen, it can recall the “memory” of the infection to produce specific antibodies and lymphocytes to prevent re-infection by the same agent. However, this “memory” can fade, and is of particular concern with RSV.

Challenge experiments have shown that 73% of adults became reinfected a second time within 26 months, and 43% became reinfected a third time with apparent symptoms in the majority of the cases (Hall et al. 1991). In short, the virus is capable of reinfecting healthy individuals, and immunity is relatively short-lived. This also makes it particularly difficult to produce a vaccine that does not need to be administered annually.

An appropriate adaptive immune response requires the activity of dendritic cells (DCs). In short, DCs are antigen presenter cells, and direct the T-cell and B-cell response at a particular target. DCs move from a site of infection to the lymph nodes in order to activate the proliferation of the proper lymphocytes to defend against a particular pathogen (a short video is provided below). DC migration is directed primarily by chemokines, or signalling proteins that the DC recognizes through the receptor CCR7. Without CCR7, the DC’s ability to detect chemokines is severely diminished, and without migration to the lymph node, downstream activation of the adaptive immune response is absent.

In the 2011 paper in PLOS Pathogens by Nouen et al., the authors demonstrate that RSV infection leads to a decrease in the expression of CCR7 in DCs during infection. RSV alters dendritic cell migration, and reduces DC migration to the lymph nodes.I This finding suggests that RSV is capable of regulating the immune response by reducing the activation of lymphocytes. Measles virus, another paramyxovirus, has also been shown inhibit DC migration through the modulation of CCR7 expression.

I would again like to highlight the incredible adaptability of pathogens to persist in an environment. Viruses have evolved to persist in even the harshest of all environments, including the human immune system, which is tasked with the very specific job of fighting these viruses.

Despite being known as a clinically significant human pathogen since the 1950s, a vaccine for RSV is still unavailable.  However, a better understanding of how RSV modulates immunity gives us a clearer picture of why RSV vaccine development is so difficult. In contrast to EbolavirusRSV is very well adapted to humans, and rarely kills its host, but the disease burden of RSV is certainly significant.

Fortunately, basic research into mechanisms of pathogenesis is leading us in the right direction. But what you may believe to be a “common cold” (which may actually be caused by any number of viruses including rhinovirus, adenovirus, or coronavirus) can be RSV. Persistent infection should have you worried, but at least it’s not Ebola.

The frightening Filoviridae

July 22, 2013 1 comment

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Ebola hemorrhagic fever is caused by Ebola virus, a filamentous virus that is part of the family Filoviridae. Ebolavirus is of particular concern to global health as a result of killing as many as 90% of its victims. The Hot Zone tells in great detail the discovery and fear driven by Filoviruses, I highly suggest it.* This high mortality can be attributed to its ability to avoid detection by the immune system. Normally the human adaptive and innate immune system are capable of recognizing specific markers, or antigens, from pathogens. These antigens trigger an immune response that can clear the infection. The adaptability and complexity of the immune system is astounding, and can be better understood with the above wikipedia links.** While the immune system plays a large role in infectious disease, the star of the game is Ebolavirus.

Viruses are characterized by their parasitism, and the inability to metabolize and replicate in the absence of a host. Because of this, viruses hijack host cell machinery in order to reproduce. But first, the virus must gain entry into a cell. Viruses have found various ways to enter their host cells. For example, HIV entry is characterized by fusion of the viral envelope to the membrane of the cell, without any endocytosis. In contrast, most viruses utilize a process of endocytosis, where fusion of the virus to the cell membrane triggers a response by the cell to engulf the virus. How Viruses Hijack Endocytic Machinery.

After entering a cell, Ebolavirus uses host proteins, along with a few of its own, to make copies of itself. These new viral copies leave the cell in search of another host to infect. However, after leaving the cell, the viral particles are exposed to the dangers of the human immune system. The mechanism by which Ebolavirus evades the immune system has been dubbed antigenic subversion. The paper by Mohan et al. at Emory University is here, and open access: Antigenic Subversion: A Novel Mechanism of Host Immune Evasion by Ebola Virus.

Viruses are subject to natural selection and evolution, similar to all organisms. Many pathogens undergo antigenic variationwhere the antigens of the microbe change such that the immune system no longer recognizes it as a pathogen, allowing it to reside in its host undetected. Alternatively, antigenic subversion is a mechanism by which Ebolavirus actively “hides” from the immune system by telling the infected cell to secrete an antigen (secreted GlycoProtein, sGP) that effectively undermines the ability of the immune system to recognize the capsid of the virus. The excreted antigens sequester the antibodies directed toward finding and clearing viral particles coated in GP1,2, the capsid glycoprotein responsible for attachment of the virus to the host cell. Without an appropriate antibody response, clearance of the virus is virtually impossible and free viral particles roam the body destroying cell after cell. This is where it gets heavy.

The translated products that contribute to antigenic subversion are a result of transcriptional editing. The viral polymerase carried by Ebolavirus is prone to slippage, and 20% of the time, the viral RNA polymerase creates a mRNA transcript that allows for the translation of open reading frames as a single protein, the fusion GP1,2 protein. 80% of the time, the polymerase creates a transcript that carries a stop codon before the second open reading frame, creating the secreted sGP protein. (PNAS Sanchez 1996)

Furthermore, antibodies against sGP harbor low reactivity with GP1,2. However, antibodies against GP1,2 react strongly with sGP. Because sGP is simply a truncated version of GP1,2, this suggests that the conformations of sGP create epitopes that differ from those on GP1,2. These conformational changes alter the immune response, leading to the production of antibodies that can strongly opsonize sGP, but weakly bind GP1,2.

Many pathogens employ a decoy mechanism, where they create an antigen that absorbs the effects of the antagonizing antibodies. However, this differs in that the “decoy” antigen is not only sequestering antibodies, but also altering the immune response to create ineffective and poorly protective antibodies against sGP when the immune system would be better off producing anti-GP1,2 antibodies.

A 3 minute discussion about the entry of Ebolavirus:

*A crappily formatted, but readable, PDF version of the book is here.

**I tried to keep it concise, but introduction to viruses is no brief task. I should do a pathogen 101, in addition to an immune system 101. I would like to delve into specific molecular mechanisms, but it’s easier to think about than it is to write about. Next time.