Monday, April 30, 2018

The Fast and the Furious...Antibiotic Discovery

Over 10 million deaths per year. That's the global death toll experts predict from drug-resistant infections by 2050 without new ways to combat these microbes. Unlike most disease areas, where new and improved drugs are being discovered and developed every year, bacterial infections are still largely treated with classes of antibiotics that were discovered over 50 years ago. Many of these drugs were found by screening microbes that live in the soil, which has proven to be a successful strategy for obtaining a vast variety of chemical compounds. However, most microbes in soil cannot be grown in the lab, leaving large gaps in our ability to study them and identify potential new antibiotics. Recent advances, however, have helped overcome this problem and lead to the identification of the first new classes of antibiotics in 30 years.

The iChip culture method.
Al Granberg. https://www.the-scientist.com/
?articles.view/articleNo/44049/title/Cultural-Riches/
In 2015, a team of scientists at Northeastern University isolated a new antibiotic using an ingenious method for growing soil microbes with the iChip, a device with wells for bacteria that are separated from a natural environment (like soil) by a diffusion membrane with tiny pores that allow the transfer of nutrients without allowing the bacteria to leave the well. Using this method, researchers were able to isolate new chemical compounds from these bacteria and identify teixobactin. Upon further testing, they found that teixobactin was highly effective at killing several types of bacteria in culture, including Mycobacterium tuberculosis and methicillin-resistant Staphylococcus aureus (MRSA), by interfering with the ability of the bacteria to build cell walls. Teixobactin was also shown to be effective at clearing infections in mice. Although teixobactin itself is difficult to produce, a group at the University of Lincoln, UK, recently synthesized a much easier-to-make version that maintains potency and could be used for commercial production.


In 2017, another new class of antibiotics was discovered at Rockefeller University using just bioinformatic analysis of DNA extracted from the environment; this group didn’t even have to grow the bacteria in the lab. They based their strategy on the knowledge that there is a family of calcium-dependent antibiotics. By isolating DNA directly from environmental samples and searching for sequences that featured the known calcium-binding signature, they could identify genes that potentially encoded new calcium-dependent antibiotics. They then transferred these DNA sequences into bacteria that can be cultured for further study. The new antibiotic class they found, the malacidins, also interferes with the ability of bacteria to properly form cell walls. Malacidins were shown to clear MRSA infections in the cut wounds of rats. Importantly, even after 3 weeks of exposure to the drug, there was no sign of resistant bacteria. This finding suggests that the mechanism of action for the malacidins is one that cannot be circumvented easily by the bacteria, which bodes well for their use against multidrug-resistant pathogens.

A third novel class of antibiotics was just described earlier this month in the journal Molecular Cell by researchers from the University of Illinois at Chicago and the biotech company Nosopharm. This class, called the odilorhabdins, was isolated from a bacterium that lives in a symbiotic relationship with a nematode worm in soil. This bacterium secretes a number of compounds that help the nematode colonize and kill insects and keep the insect carcass from being invaded by other bacteria or fungi. The odilorhabdins exert their antimicrobial activity by interfering with bacterial protein production. While several other antibiotics also target this process, the odilorhabdins bind to a unique site on the bacterial ribosome (the part of the cell responsible for making proteins); this means that bacteria that are resistant to other antibiotics that interfere with protein production will not be resistant to the odilorhabdins. When tested for their ability to kill several pathogenic bacteria in culture, the odilorhabdins were highly effective. One of the odilorhabdins, NOSO-95179, was also tested in mice and could significantly reduce Klebsiella pneumoniae septicemia and lung infection.

MRSA (green) being enveloped
by a white blood cell.
CDC's Public Health Image Library.
Image # 18126; photo credit: NIAID.
While these new antibiotics are still in the early stages of development and are at least 6-10 years from being available for use in people, the rapid identification of multiple new antibiotic classes after a decades-long “discovery void” provides hope. The new techniques for culturing soil bacteria, along with bioinformatic approaches that avoid this step all together, offer new avenues for drug discovery. Additionally, there is ongoing work to re-investigate previously sidelined drug candidates and modify existing antibiotics to improve their efficacy and overcome resistance. No matter the approach, the road to develop a new antibiotic is long and expensive, making it impossible for academic research labs to go it alone. Luckily, pharmaceutical companies are beginning to get more involved. In 2016, the Antimicrobial Resistance Industry Alliance presented the “Davos Declaration” at the World Economic Forum. Nearly 100 companies signed the declaration, pledging to support the research and development of new antimicrobials and improve access to current and future treatments. With this renewed commitment from the pharmaceutical industry, which had largely been turning away from antimicrobial development in recent years, the financing and man-power to produce these new antibiotics might just be available. While nothing short of a strong, concerted effort to deal with drug resistance will allow us to avoid the looming projection of 10 million deaths per year, the current pace of advancement bodes well for our ability to rise to the challenge.

Thursday, March 29, 2018

New funding (and new hope) for a Lassa virus vaccine

Nearly 2 years ago in 2016, I wrote a post about a deadly virus that was causing a worrying outbreak in Nigeria: the Lassa virus. For the rest of 2016 and 2017, the outbreak lessened in severity, but it was not completely eliminated. Unfortunately, this year has featured a new surge in infections with the virus. In just the first 2 months of 2018, at least 317 people have been infected with Lassa virus, far surpassing the 143 cases confirmed in all of 2017. Additionally, around 20% of those infected in 2018 have died from the infection.

While the reports from March suggest that the current outbreak is slowing, major hurdles for the containment and management of Lassa fever cases still exist. The disease is carried by multimammate rats, which are difficult to keep out of homes and away from human food, especially as populations in Africa grow and the once-empty fields where the rodents live are developed. The long asymptomatic period at the beginning of infection makes it difficult to diagnose and treat effectively. Even once symptoms do manifest, they tend to be mild and non-specific, with 80% of those infected suffering from mild fever, general malaise, and/or headache. Additionally, the sub-optimal treatments have not improved in recent years, and there is still no vaccine.

lassa, virus, virions, adjacent, cell, debris, virus, member, virus, family, arenaviridae
Lassa virus particles. CDC's Public Health Image Library.
Image # 8700; photo credit: C.S. Goldsmith.
In an attempt to deal with these issues, the Coalition for Epidemic Preparedness Innovations (CEPI) awarded $37.5 million to Themis Bioscience earlier this month for the development of their Lassa virus vaccine. CEPI was created in the wake of the Ebola epidemic and receives funding from the Wellcome Trust, the Bill & Melinda Gates Foundation, the European Commission, and the governments of Germany, Japan, Norway, Belgium, Canada, and Australia to support the development of vaccines for potential or existing pandemics. While there are many diseases that could fall into this category, the main focus in the next 5 years for the group will be Lassa virus, the Middle East Respiratory Syndrome (MERS) virus, and Nipah virus.

With the funding from CEPI, Themis plans to move into human trials with their Lassa virus vaccine as early as this year. Following the Ebola crisis, the World Health Organization developed a procedure to fast-track the approval of products for use in public health emergencies. The hope is that these procedures could be used in the context of the Lassa virus outbreak to accelerate the development of the Themis vaccine. To further speed development, the Themis Lassa virus vaccine will be based on the measles vaccine vector previously created by the Institut Pasteur, which has already been used effectively in humans. By inserting Lassa virus proteins into this vector, a new vaccine that will prime the body to respond to a Lassa infection will be created. This strategy opens the door to allow for the rapid creation of additional vaccines, as well.

The funding from CEPI will support the preclinical and initial clinical development through a phase 2 trial of the Themis Lassa virus vaccine in order to test its safety and efficacy. The ultimate goal is that the funds will allow the production of a vaccine stockpile that will be ready to test in an outbreak, which may be needed sooner rather than later. While the current outbreak appears to be slowing, and the dry season, when the majority of Lassa fever cases in Nigeria have historically occurred, is coming to an end, a report from Sierra Leone has suggested that the incidence of Lassa fever may actually be higher during the rainy season. This leaves uncertainty about the outlook for the current Lassa fever outbreak. But whether the outbreak continues now or goes dormant for the next 10 years, a vaccine will be a vital weapon in the fight against Lassa virus for the future.

Monday, March 5, 2018

Good reason for my writing gap

I must apologize for my extended absence from writing these posts. But I promise I had good reason! Since my last post at the end of August, I've completed my dissertation and graduated with my PhD, hunted for a job, gotten a job, moved, and started that new job. But now I'm back and ready to provide you all with more exciting biology posts. Enjoy!

Flu vaccination: Arm yourself against the anti-vax arguement

The flu vaccine. Always a hot topic, especially in years when the vaccine has poor efficacy as it does this year. At times like this, the anti-vax community can gain leverage. So let's take a look at some of the top arguments used in the anti-vax movement and see if we can shed some light on the controversy.


The flu vaccine makes you sick.
People will often say that they got the flu because of the flu shot. This is actually not possible. The flu shot is made with an inactivated, DEAD form of the virus that cannot replicate and transmit. While there can be side effects from the shot that make you feel "sick," this is not the flu. Additionally, the flu vaccine stimulates your immune system, which actually strengthens your ability to fight infections and avoid getting "sick." It is important to note, though, that getting the flu vaccine does not mean you are immediately protected. It typically takes about two weeks to gain the full advantage from the vaccine. People who were already exposed to the virus before receiving the vaccine or who are exposed shortly after vaccination will not be protected.
Image result for flu vaccine
Brian Snyder/Reuters/Landov

The flu vaccine contains mercury that will poison you.
Flu shots that come from a multi-dose vial do typically contain thimerosal, an ethylmercury-based preservative to prevent any bacteria or fungus from contaminating the vaccine. Flu shots that come in prefilled syringes and the nasal flu vaccine do NOT contain this preservative (with the exception of the Fluvirin prefilled syringes from Seqiris, which contain trace amounts of thimerosal). It is important to note the distinction between ethylmercury (found in thimerosal) and methylmercury. Methylmercury is the form of mercury found in foods, like seafood, that is associated with neurological complications. While in vitro studies (in cell culture systems and not in the body) have found little difference between the effects of methyl- and ethylmercury, the story is quite different in vivo (in actual living creatures). Ethylmercury is cleared from the bloodstream significantly more quickly than methylmercury, minimizing the exposure of the body to mercury. Ethylmercury is also compartmentalized by the body more successfully than methylmercury, further limiting exposure. Some may argue that based on the in vitro evidence, ethylmercury is unsafe, but the in vivo data and years of studies have shown that this is not the case. But, if you still want to avoid mercury all together, you can get a prefilled syringe version of the flu shot that contains no thimerosal.

The flu vaccine causes the virus to mutate, becoming more virulent.
This is a popular argument used in the anti-vax community. While that is always a theoretical possibility, there is currently no scientific evidence that this is happening. The influenza virus has an extremely rapid mutation rate, whether you put selective pressure on it or not, so it’s going to be mutating all the time regardless of what we as humans do. This is just the nature of the virus’s replication; the enzyme it uses to replicate its genome makes a lot of mistakes, and the virus is perfectly happy to continue on with those mistakes (aka mutations).

The idea that vaccines create more virulent viruses is typically based on the fact that the use of antibiotics can lead to more pathogenic bacteria, which has been observed. But the vaccine works very differently from an antibiotic. In the case of bacteria, they directly come in contact with and are affected by the antibiotic, which gives bacteria that can survive while in contact a direct advantage. In the case of the vaccine, since it is priming an individual’s immune system and not directly contacting the virus, there is no such direct advantage to the virus. Even if the influenza virus you encounter is different from the vaccine strain, your immune system will be primed and you will have a better chance of successfully clearing the virus. While it is theoretically possible that by vaccinating, you remove the predominant influenza strains, leaving an opening in the environment for a “resistant” strain to fill, most of the highly virulent and dangerous strains have emerged in parts of the world where vaccination rates are very low, so this doesn’t seem to be happening.

Vaccination causes super strains of the flu virus to emerge that are immune to our vaccines. 
Image result for flu vaccine
Influenza virus. Carrington College
People often further argue that our lack of vaccine effectiveness in recent years comes from the emergence of “super” strains of the virus that are “immune” to our vaccines. But the research suggests otherwise. Vaccinemakers use a less-than-ideal system for choosing the vaccine strains that relies on a test using ferrets exposed to the virus. This can lead to incorrect selection and a poor vaccine. Also, improved diagnostic techniques make it more likely for us to capture influenza infection than ever before, so people who would have been diagnosed with some unknown viral disease (and therefore considered “protected”) in the past are now being properly diagnosed as influenza patients. And we are learning that our vaccine production system making the vaccine in eggs leads to its own set of mutations in the vaccine strain that often dampen protection in people. A lot of groups are working to improve the vaccine production pipeline and find alternative ways that don’t involve growing the vaccine in eggs, so that will likely be the way of the future in 5-10 years.

Vaccines cause autism.
This claim is not unique to the flu vaccine and has been spouted at the forefront of the anti-vax community ever since 1998, when Andrew Wakefield and colleagues published a study looking at 12 children that claimed there was a link between the measles-mumps-rubella vaccine and autism. What people in the anti-vax community typically fail to realize is that since that article was published, it has been retracted (the authors themselves admitted their conclusions were inaccurate), Wakefield and colleagues have been found guilty of ethical violations and fraud, and Wakefield has been removed from the UK medical registry. They hand-picked the patients for their study and falsified data to ensure that they would conclude there was a link between vaccines and autism. Additionally, they had received funding from lawyers who had been hired by parents to bring lawsuits against vaccine companies. Since the Wakefield study, many large-scale studies have been performed to see if their initial findings could be confirmed in spite of the ethical issues with the study, but no corroborating evidence has been found. The link between vaccination and autism is based on fabricated data and has no true scientific merit.


In spite of the potentially poor efficacy, healthcare providers will still push for vaccination. Any protection is better than none, especially if you are in contact with the populations at high-risk of dying from infection, i.e. the elderly, babies, and immuno-compromised individuals. The more people who are protected (even if the protection is sub-optimal), the less likely it is for the virus to come in contact with these highly susceptible individuals, and healthcare providers rely on this to keep patients safe. The bottom line is we may have a sub-optimal vaccine, but a lot of people are actively working on that, any protection is still better than none, and there is no evidence that getting the vaccine has any negative impacts on the pool of viruses we are exposed to. So please do not be discouraged, and use your new flu vaccine knowledge to help educate others!

Thursday, August 31, 2017

The mosquito microbiome: An ally in the fight against disease

The annoying buzz of pesky little mosquitoes. At this time of year, the sound can be heard in backyards all around the world. Due to emerging threats like Zika and Dengue virus, people are becoming more and more familiar with the harm these little devils can cause. While vaccines and treatments for many mosquito-borne illnesses remain elusive, some researchers are placing new hope in other micro-organisms who may be able to play a role in preventing these dangerous diseases.

Previous work focused on malaria and its vector, the anopheline mosquitoes, has implicated micro-organisms, such as bacteria or fungi, within the mosquito to have an effect on the mosquito's ability to transmit the disease. Numerous studies in both Anopheles stephensi and Anopheles gambiae have shown that microbes in their midguts can influence the malarial parasite's ability to develop and transmit to new hosts. This is also not a new concept in the Aedes mosquitoes, the vectors for many of the mosquito-borne viruses. Wolbachia bacteria have been successfully introduced multiple times into these mosquitoes to prevent infection in the past.

Most previous studies have focused on introducing microbes to adult mosquitoes. In the field, this naturally presents challenges with application as adult mosquitoes are constantly migrating from place to place. However, recent work highlights that similar strategies could be used on mosquito larvae to influence their ability to transmit disease as adults. Larvae are much more targetable, due to the relative ease of identifying larval development sites.

In the latest study of the mosquito microbiota and its effects on vectorial capacity (the ability of a vector, like the mosquito, to transmit a particular disease), researchers found that differences in bacterial colonization of larvae could have an effect on the adult mosquito's traits. This means that by changing the bacteria larvae are exposed to, you could influence their ability to transmit disease as adults.

While there are many environmental concerns that will need to be addressed before a strategy altering the bacterial make-up of mosquito breeding sites, this new study and the growing body of work focusing on the mosquito microbiome's effects on vectorial capacity offer hope for new strategies to control disease spread. Perhaps some day we will be able to add a simple pellet of bacteria to a pool of water with mosquito larvae and prevent all the subsequent adults from transmitting disease. This may seem like a far-fetched dream today, but with continued research, it could one day be a reality.

Monday, July 31, 2017

New diagnostic method may help fight antibiotic resistance

Coughing, sneezing, runny nose, wheezing; respiratory tract infections are extremely common, with the average American adult enduring two to four each year. Typically, the symptoms last for seven to ten days while you struggle through, and then you get better. If you go to a doctor with these symptoms, they will likely prescribe you a broad-range antibiotic. This may sound fine, but there is a big issue with that: not all respiratory tract infections are caused by a bacterial infection. Over-use of antibiotics has been leading to increased antibiotic resistance for decades. The only way to prevent the over-prescribing of antibiotics for these respiratory tract infections is to determine the cause of each infection. Unfortunately, current technologies for diagnosing these infections are not fast and specific enough to allow timely and proper diagnosis. New technology has emerged that may help with the diagnosis and cut down on the over-use of antibiotics.

When exposed to different pathogens, the body's immune system responds in different ways. A virus, for example, causes cells to react in a different way than a bacterium. The cells of the immune system that can be found in the blood can be profiled to understand what type of infection they are fighting. This has been done by studying the messenger RNAs (mRNAs), also known as transcripts, found within monocytes, a specific subset of immune cells. mRNAs lead to the proteins being made by a cell and often play key roles in regulating the activation of pathways involved in an immune response. A recent study identified ten different mRNAs that could be used to determine if the body was responding to a bacterial or a viral respiratory tract infection. A more recent study further validated these ten mRNAs by confirming their use in 94 hospitalized adults with respiratory tract infections and identified even more mRNAs that could differentiate a bacterial infection from a viral infection. This allows for more appropriate use of antibiotics in these patients and avoids the potential over-use of antibiotics that threatens their effectiveness.

As more and more antibiotic-resistant infections emerge, it is becoming more important than ever to safeguard our potent antibiotics by only using them when necessary. When antibiotics are used, they kill off whatever bacteria are susceptible to their effects, leaving behind only those that are resistant. This helps select for antibiotic-resistant bacteria within a population. The over-use of antibiotics has sped this natural selection process, allowing for the rapid development of resistance even to the newest antibiotics. Using technologies such as this transcript profiling of immune cells will help slow the selection process by ensuring antibiotics are only introduced when they can be of help, allowing our antibiotics to maintain their usefulness longer before resistance develops.

The technology to profile transcripts of immune cells in the blood has the opportunity for application far beyond the identification of bacterial versus viral respiratory infection. Individual pathogens themselves can produce unique immune profiles that could one day be categorized using similar methods. With the standard diagnostics of the past, it is nearly impossible to diagnose a bacterial or viral infection unless the bacteria can be cultured or the virus can be isolated. Knowing the unique transcript profile induced by a pathogen could someday allow for molecular diagnosis of a number of pathogens without the need to culture the bacteria or isolate the virus, allowing for an even more significant reduction in antibiotic over-use. This would also provide more rapid diagnosis; transcript analysis could be performed in a matter of hours, while the diagnostics of the past frequently require days. With emerging technologies, these goals become even more achievable every day, and we may soon see a time when antibiotics are only used for infections confirmed to be caused by a susceptible bacteria.

Thursday, June 29, 2017

More vaccination victories needed in the meningitis fight

Vaccinations have been proven time and time again to prevent disease and improve health outcomes. All around the world, vaccines have been deployed to deal with illnesses as common as the flu and as deadly as Ebola. Meningitis is another disease for which vaccination has become a major priority. The “kissing disease,” at it is sometimes called, has made a number of appearances on college campuses across the United States. While incidence in the U.S. remains quite low, at 0.3-4 cases per 100,000 persons, incidence can be as high as 1 case per 100 persons in the “meningitis belt” of Africa, where epidemics occur with regularity.

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Neisseria meningitidis, the bacterium responsible for meningitis.
Image from Bioquell.com
Infection with the bacterium Neisseria meningitidis, the major cause of meningitis, often goes unnoticed. The bacteria take up residence within the nasal cavity, where they can stay without causing disease in a carrier individual. However, in approximately 1-5% of people exposed to the bacteria, invasive disease occurs, and the bacteria enter the bloodstream, leading to life-threatening disease.

Symptoms of meningitis typically begin almost immediately, just one day after infection, and include flu-like symptoms of fever, headache, and stiffness. Because the bacteria enter the bloodstream, any organ or tissue can become infected and impaired. Despite years of research, mortality rates continue to range from 10-15%, even in developed countries, with rates above 20% in the developing world. Even for those who survive the invasive disease stage, meningitis causes lasting impairments in 19% of patients, with neurological disabilities, seizures, hearing or visual loss, and cognitive impairment being classical manifestations. The rapidity of disease progression, along with the high mortality rate, make meningitis a prime disease target for vaccination.

The first vaccines against meningitis were developed in the 1970s. Unfortunately, these early vaccines lacked the ability to maintain long-lasting immunity against the bacteria. In the late 1990s, alterations were made in the vaccine components, allowing for the elicitation of an immunological memory response that would be effective to protect young children into their adult years and would even help reduce the rates of carriage of the bacteria in the nasal cavity. While this was great news for the prevention of meningitis, challenges still remained. The bacteria that cause disease can belong to any of 6 different serogroups, meaning that immunity to one serogroup will not necessarily provide protection from another. This requires differential targeting of all 6 serogroups to truly prevent disease.

Image result for meningitis vaccine
Image from the Meningitis Vaccine Project
Researchers have addressed this challenge by producing different vaccines for use in specific parts of the world where each serogroup is problematic. In the meningitis belt of Africa, for example, serogroup A has historically been the cause of epidemics. To wipe out these epidemics, a mass vaccination campaign was begun in 2010; the Meningitis Vaccine Project produced and provided vaccines against N. meningitidis serogroup A for over 217 million people in 17 different countries. Thanks to these vaccines, epidemics linked to the serogroup A bacteria have been eliminated.

Unfortunately, when one serogroup is removed, a niche opens up for another. Just last month, the CDC announced that a small epidemic in Liberia had been caused by the N. meningitidis serogroup C bacteria. Nigeria and Niger have also reported outbreaks of this serogroup. Luckily, in the case of Liberia, the country’s response time was extremely rapid. Thanks to the health system improvements made during the Ebola outbreak, Liberia now has a robust case detection and monitoring system. Other countries in the area, however, are not nearly as advanced and could suffer a severe epidemic if serogroup C moves in with force.


Great strides have been made in the fight against meningitis outbreaks. However, the complexity of the group of bacteria responsible for the disease leaves a number of challenges in place that must be overcome. The ideal solution would be the introduction of a vaccine that combined pieces from each bacteria serogroup to produce an immune response in patients that would protect from all six serogroups at the same time. While some quadrivalent vaccines already exist, which provide protection against four of the six serogroups, these vaccines have only been recommended for use in the U.S. for adolescents entering college. Protection from this vaccine only lasts 2-5 years in adults, making it less than ideal for deployment in rural areas where boosting is not a viable option, such as Africa. Advances in vaccine technology may help improve the longevity of protection, making multivalent vaccination a more robust solution to the meningitis problem. Until then, rapid case detection and monitoring capabilities, such as those displayed in Liberia, will be the key to keeping meningitis epidemics in check as they arise. Between vaccine and monitoring advances, meningitis epidemics may one day become a thing of the past.