More than just vaccines

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Tuning down the immune system could improve the flu vaccine

This post is based on an article I recently wrote for an internship application, so it’s more formal than a typical post, but I think it’s a cool story that helps explain how the flu vaccine works. Enjoy! And stay healthy!

After more than 2,000 confirmed cases and over twenty deaths, the 2013-14 flu season is still approaching its peak.  Vaccination remains the best prevention despite the flu vaccine’s hit-or-miss reputation.   Each year the U.S. Food and Drug Administration recommends three strains of influenza that the World Health Organization believes are worth targeting, and six months later the season’s new vaccine is distributed.


This nasty viral particle is trying to get inside a cell. It’s covered in NA (red) and HA (blue) proteins.

One of the flu vaccine’s biggest problems is its inability to induce immunity against multiple viral subtypes.  Subtypes of the influenza A virus, like H1N1 or H5N1 are distinguished by the surface proteins hemagglutinin (HA) and neuraminidase (NA).  The vaccine can protect against a few subtypes at a time, but if a subtype not included in the shot makes a strong appearance one season, not much can be done to prevent it from spreading.  This year, the vaccine is pretty spot on. It includes H1N1 which has been making a comeback this year.

This problem has driven researchers to pursue a universal vaccine that could protect against multiple subtypes.  This type of protection is called heterotypic immunity.  One group of scientists from St. Jude Children’s Research Hospital hit on an unexpected way to expand the reach of one flu vaccine to multiple subtypes.  Dr. Maureen McGargill and her group published their study in Nature Immunology in December.  They studied how a common immunosuppressive drug called rapamycin influenced the ability of vaccinated mice to generate heterotypic immunity.  They vaccinated mice with one viral subtype and infected them with three other lethal subtypes.  Surprisingly, the mice who got rapamycin were better able to resist infection by all the subtypes, including an altered H5N1 strain, commonly known as the avian flu.

Rapamycin is commonly used to dampen the immune system to prevent organ transplant rejection.  It blocks an immune system regulating protein called mTOR.  Three other animal vaccine studies previously found that rapamycin enhanced generation of memory T cells, cells that can remember a virus and kill infected cells when they detect viral proteins.  None of these studies linked higher numbers of memory T cells to protection from infection.  McGargill’s group observed both higher memory T cell numbers and better protection, but could not link the two. Rather, they found that protection was related to changes in the kinds of antibodies that the vaccine induced.

The flu vaccine contains pieces of viral proteins called antigens and mice and humans make antibodies that specifically bind these antigens on the viruses and neutralize them.  The more specific the antibodies are though, the more they drive those proteins to mutate so the virus can escape detection.  This shape-shifting tactic is called antigenic drift, and it is part of the reason it is so difficult to predict which vaccine formulation will be most effective each year.    

The coveted universal vaccine would induce antibodies that recognize parts of the virus that are shared, or conserved, by many subtypes and unlikely to mutate.  But B cells, the cells that make antibodies, tend to make more and more specific antibodies over time.  Over several weeks, B cells go from making weak, broadly binding antibodies that can cross-react with many subtypes, to strong and specific ones.   McGargill and her colleagues found that rapamycin interrupted this process and caused the mice to make more of the broadly binding antibodies.  The antibodies also targeted different parts of the hemagglutinin protein.

The group could not determine exactly how the altered antibodies contributed to protection from infection.  They concluded that the antibodies produced after rapamycin treatment were less specific and therefore able to cross-react with several viral subtypes.   As a result, the treated mice were less susceptible to the three different influenza subtypes.

These findings could be useful for quickly designing broadly protective vaccines in the face of a new subtype outbreak or epidemic.  It currently takes about six months to manufacture the annually recommended formulation.  A heterotypic vaccine would not be as dependent on the World Health Organization’s laborious surveillance and data analysis, and could be stored and used for many flu seasons.


Bridges CB et al. Effectiveness and cost-benefit of influenza vaccinations on healthy working adults: A randomized controlled trial. JAMA (2000) 284:1655-63.

Keating R. et al. The kinase mTOR modulates the antibody response to provide cross-protective immunity to lethal infection from influenza virus.  Nature Immunology (2013) 14:1266-76.

McMichael A and Haynes B. Influenza vaccines: mTOR inhibition surprisingly leads to protection. Nature Immunology (2013) 14:1205-07.

Pica N and Palese P. Toward a universal influenza virus vaccine: Prospects and challenges. Ann. Rev. Med. (2013) 64:189-202.


Norovirus! (AKA the 24 hour stomach bug) Can it be avoided?

The other day I found myself in the break room near my lab eyeing a container of chocolate-covered nuts left over from the Christmas holiday.  Someone left them out as a treat for foraging graduate students and post-docs.  I stood for a moment holding a single piece in my fingers and as I was about to put it into my mouth, I remembered—Norovirus!

I had no reason to think the nuts could be a reservoir of norovirus, but I did have good reason to avoid shared uncooked food with an unknown history.   A good chunk of my family had just had their holiday ruined by the virus, sometimes known as the 24-hour bug or stomach flu.  It causes gastroenteritis, or inflammation of the gut, complete with diarrhea, vomiting and overall exhaustion.  It can only be transmitted via stool or vomit, and though there was certainly none of that visible in the bin of delicious looking nuts, I began to think of all the hands that may have been inside. If it came from a family holiday party, some of those hands may have belonged to kids who haven’t yet learned to wash them for a full 30 seconds after using the bathroom. I threw the candy away, closed the container and left the break room.

I may have avoided norovirus that day by a judicious food choice, but not everyone has that moment of doubt before sharing a drink, holding a child’s hand or ordering a deli sandwich.  It is sometimes just unavoidable, especially because it’s contagious for up to two weeks after the first horrible 24 hours. The center for disease control estimates that 19-21 million people are infected with norovirus each year and it’s actually responsible for somewhere between 600 and 800 deaths per year. Those most vulnerable are either over 65 or under 5 years old.

These figures are driving researchers to search for a vaccine, even if just for those most vulnerable or during outbreaks.  But norovirus, or I should say noroviruses are particularly complicated. They are split into 5 groups (I-V) based on how similar their DNA sequences are. Those groups, called genogroups, are split into anywhere between 8 and 30 genotypes and those can be further divided into variants.  The classification is complicated enough to require the use of a software program that compares genome sequences.

Only three of the genotypes can infect humans and the strain GII.4 has been the most common cause of outbreaks since the early 2000s.  For decades before that, a different strain dominated, and the power structure may shift again.  The abundance of genotypes and variants and their changing frequencies in communities make vaccine design a daunting task.  On top of that, researchers are still discovering new genotypes and variants.  In 2012 a strain called GII.4-Sydney was identified in Australia and made its way to the UK and the US within a year.

Norovirus 4

Up close scanning electron microscopic image of norovirus particles

There is evidence that infection with norovirus can generate immunity in some people, meaning that once they get infected, they are protected from re-infection for some weeks or months. However, no one knows how all of the viral subgroups and variants might affect immunity and vaccine design. In a study published in September, researchers from the University of Florida infected mice with one of two closely related norovirus strains and found major differences in the immune responses.

One of the two strains was much better at activating a class of immune cells called antigen presenting cells. These include dendritic cells and macrophages, and they are experts at displaying pieces of virus and training B and T cells to respond to the infection and turn into memory cells. As a result of the enhanced response, infected mice were protected from a reinfection six weeks later.

{Researchers determine “protection” by measuring how much virus shows up in an animal’s organs after infection. In this case, they measured norovirus in the small and large intestines and in the lymph nodes attached to the intestines.}

Oddly enough, the researchers narrowed down the cause of these changes down to a group of structural proteins whose sequences only varied by about 10% between the two strains.

A key finding in this study was that the protective norovirus strain protected mice from re-infection with both strains.  This is important since any vaccine against norovirus would have to protect against several strains and genotypes. It also points out specific characteristics of the immune response that make all the difference between becoming immune or getting re-infected, for example, robust antigen presentation and B and T cell memory.  A vaccine that could foster those characteristics could potentially protect people from several norovirus strains.  It may take a while to get there. In the meantime I will keep my hands clean and out of community candy dishes.


*A reader noted that the poster above says norovirus is contagious for 2-3 days, whereas I wrote above that it can be contagious for 2 weeks.  To clarify, the virus is most contagious for 2-3 days, but it can continue to be shed in stool for 2 weeks. See for more.



Zhu S., Regev D., Watanabe M., Hickman D., Moussatche N., Jesus D.M., Kahan S.M., Napthine S., Brierley I. & Hunter R.N. & (2013). Identification of Immune and Viral Correlates of Norovirus Protective Immunity through Comparative Study of Intra-Cluster Norovirus Strains, PLoS Pathogens, 9 (9) e1003592. DOI:

Hoa Tran T.N., Trainor E., Nakagomi T., Cunliffe N.A. & Nakagomi O. (2013). Molecular epidemiology of noroviruses associated with acute sporadic gastroenteritis in children: Global distribution of genogroups, genotypes and GII.4 variants, Journal of Clinical Virology, 56 (3) 269-277. DOI:

Cancer immunotherapy named Science breakthrough of the year for 2013

It was exciting to see today that Science Magazine called cancer immunotherapy the breakthrough of 2013. The author Jennifer Couzin-Frankel calls it a “breakthrough strategy” and though she admits the approach is not yet widespread, she highlights promising clinical trials that have stacked up this year. “Immunotherapy marks an entirely different way of treating cancer-by targeting the immune system, not the tumor itself,” she wrote. The article deals mainly with experiments focused on activating T cells by blocking surface proteins that shut T cells down. To learn more about other approaches, see my post about cancer vaccines.  

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Update on antibiotic resistance week: FDA makes recommendations to limit antibiotics in agriculture

I mentioned in my post on antibiotic resistance that most farm animals in the U.S. are constantly on antibiotics to prevent disease and promote growth (these two outcomes are not necessarily linked).  In the E.U. this practice was halted years ago to avoid the risk of antibiotic resistance from developing.  It seems that the U.S. F.D.A. is also going in this direction. They put out a policy that recommends suspending the use of antibiotics for healthy animals. Check out these two links to learn more:


Training the immune system to kill cancer

Have you ever heard the term “cancer vaccine?”  Are there really vaccines to prevent cancer, and do they really work? The truth is, it’s kind of a misnomer. The vaccine against herpes papilloma virus (HPV) is often called a cancer vaccine, but it’s actually a vaccine to prevent an infection that can lead to cancer.  In other cases, the term “cancer vaccine” describes a treatment that trains immune cells to attack cancer cells.  There is one FDA-approved vaccine treatment for prostate cancer, but there are ongoing clinical trials for many other types of cancers. 

One recent clinical trial for patients with glioblastoma found that a cancer vaccine approach significantly extended the patients’ lives. Glioblastoma is the most common and most aggressive type of tumor that originates in the brain, and the average survival after treatment is about a year. This vaccine approach tested at Cedars-Sinai Medical Center in LA was so significant is because it gave half of the patients about five years.  The results of the study were reported at a meeting, but the details of the trial and initial findings were published in January.

Researchers collected large numbers of white blood cells (immune cells) from the volunteers through a process called leukapheresis, which separates immune cells and returns red blood cells and other blood components back to the donor.  They were after a rare cell type called monocytes that can morph into different cell types depending on their environment. Monocytes originally come from the bone marrow and remain round and smooth as they roll through the blood. Given the right signals, they can leave the blood for other tissues and change into macrophages or dendritic cells, both rugged spindly cells that poke out tiny arms to sense their environment.  

If you put white blood cells in a culture dish, as the scientists at Cedars-Sinai did,  the monocytes will stick to the bottom of the dish in just a couple of hours. Then you can wash away all of the other cells and keep just the monocytes. After about a week, they will morph on their own into macrophages—cells that eat up pathogens or other dead cells.  But if you add a couple of signaling proteins called cytokines, the monocytes will become dendritic cells.

Dendritic cells also eat up foreign material, but they are somewhat more refined at it. They break down everything that they eat and then present little pieces of it to educate other immune cells about what is going on in the body. T cells are their main pupils, and have receptors that sense what the dendritic cells are displaying.  Then both types of cells can make proteins to attack the foreign material (bacteria, cancer cells, infected cells) and signal other cells to start a cascading immune response.

Our bodies use this process to fight infection and to prevent cancers from developing. But once a tumor is formed, tumor cells are very effective at re-educating T cells and other immune cells.  Tumor cells can make proteins that lull and calm immune cells so that they can’t respond or don’t recognize the tumor cells as foreign. Technically, cancer cells aren’t foreign, but mutated and rebellious.  Proteins displayed on cancer cells can be distorted or can be made in excess, distinguishing them from normal cells.

File:Dendritic cell therapy.png

By Simon Caulton. This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

The idea behind cancer vaccines is to prepare dendritic cells outside of the body and put them back in where they can push immune system toward actively attacking tumors. The researchers at Cedars-Sinai coaxed monocytes into becoming active dendritic cells in culture. Then they gave the cells peptides, or pieces of proteins, that resembled the ones made in high abundance on glioblastoma cells.  Years of research went into simply identifying exactly which proteins were overproduced by these cancer cells and which would best activate the dendritic cells.  This study used six peptides to activate and train the dendritic cells.  Then the cells were sent back into the patients near their lymph nodes, which are full of T cells awaiting instructions.

Variations on this method are being tested for breast cancer, melanoma, leukemia and many other cancers. The outcomes will depend on which peptides are used, which peptides are made by each person’s tumor, how well one’s cells grow in culture and respond to activation and other variables. It’s a simple idea—to use the body’s own defenses to fight cancer—but there is a lot more to learn about this fascinating and promising treatment.


The National Cancer Institute 

Vaccine promises longer survival for brain tumor patients, Belinda Weber Medical News Today, Nov 2013

Phase I trial of a multi-epitope-pulsed dendritic cell vaccine for patients with newly diagnosed glioblastoma, Phuphanich S, Wheeler CJ, et al. Cancer Immunol Immunother. Jan 2013


I missed antibiotic resistance awareness week!

Last week, Europe, Australia and the U.S. all launched their 5th Antibiotic Awareness Weeks, spreading the word about bacterial resistance to antibiotics. I heard of the event during a conversation about the death of a New Zealand man who had been infected with pan-antibiotic resistant bacteria.  According to reports, the infection was not the cause of his death, but it made news because his doctors found that no known antibiotic could stop his infection.

On her blog, Superbug, writer Maryn McKenna closely follows the growing issue of antibiotic resistance. She also recently wrote a report about what the world might look like without any working antibiotics. Recall any time you’ve taken antibiotics for an ear infection or after a root canal or a simple surgery. Those simple infections and procedures could become a lot more dangerous without the ability to kill off bacteria.  After all, the first test case for penicillin was a gardener who was dying of an infection caused by a small cut from a thorn.

A very well illustrated CDC report estimated that 2 million people are infected with antibiotic resistant bacteria in the U.S. each year.  In an effort to bring some organization to the overwhelming issue, the report ranked 18 resistant organisms as “urgent,” “concerning” or “serious” threats.

What does resistance mean exactly? And what does this have to do with immunology?

Our immune systems have a variety of techniques to address bacterial infections. We have cells called phagocytes that eat bacteria and digest them, we have specialized T cells, natural killer cells and neutrophils that secrete molecules and proteins that damage bacteria or kill infected cells. Proteins in our blood (complement proteins) stick to bacterial cell surfaces and then build upon each other like blocks until they make what’s called an “attack complex” that drills a hole in the bacterial cell membrane. 

{Did you know we need free radicals to fight infections and kill cancer cells?  Phagocytes use them to kill the bacteria that they engulf.  Many people think of free radicals as “bad” molecules and take antioxidants hoping to prevent cancer, but free radicals are one way our bodies destroy rebellious cancer cells. In fact, many cancer treatments activate free radicals to target cancer cells and patients receiving these treatments are instructed to avoid antioxidant supplements.}

If a species of bacteria is good at avoiding one tactic, there are plenty of others, and a healthy immune system will usually contain an infection and eliminate it. If someone has an unhealthy immune system (immunocompromised) or the inflammation from the immune response starts to damage tissue, antibiotics are a great way give the immune cells a fighting chance and spare the infected person.

Unlike the immune system, an antibiotic is just one compound with one tactic or mechanism. So it’s possible for just one mutation to give a bacterium resistance to that one compound’s tactic. If a drug targets a protein needed for bacterial cell membrane construction, the bacteria may alter the protein, change its construction method or make a different protein that pumps the drug out of the cell.

DNA mutations are common at the rate that bacteria divide.  Staphylococcus aureus, for example, can divide every half hour. I grow S. aureus in the lab, and when I put an amount that could fit on a pen point into a tube of special broth at 37° C (the same temperature as the human body), the next day I end up with enough bacteria to fill about a quarter of a teaspoon.

Life for bacteria is tougher inside a human body since they are always being attacked by the immune system. But say the bacteria get the upper hand inside an infected person, we’ll call her Amy. Amy goes to the doctor and gets an antibiotic prescription, perhaps methicillin or vancomycin—enough pills to take one a day for 7 days. When she starts taking them many bacteria will die or stop dividing and her immune cells will be able to make headway against the infection.  S. aureus can accumulate hundreds of mutations a day and even though most of the mutants will die, there will likely be individual bacterium inside of Amy with mutations that make them resistant to the drug she is taking. Those resistant mutants have an advantage over the other bacteria and will take over as all of their siblings get killed off by the drug.


Imagine the image shown on a kitchen cleaner commercial as it touts “kills 99.9% of germs.” On one side of the screen the “before” shot shows lots of wiggly cartoon “germs” and on the other side, after the cleaner is used, there are one or two wiggly little guys left.  By “99.9%,” the commercial means that their product kills most known household species of bacteria, but if those were all the same species infecting a person and the cleaner was an antibiotic drug, those two little guys left behind would multiply with a vengeance and birth a resistant strain.  There is a potential for that to happen every time a person takes antibiotics.

Ideally, even if mutations do arise, the antibiotics slow down the bacteria enough to let the immune system completely eradicate the infection (including the resistant mutants).  But say Amy takes her prescription for 4 days and feels like she’s back to normal so she decides not to finish the whole 7 day course. By this time, she may be harboring resistant mutants and when she stops taking the drug, her immune system will suddenly have a lot more to deal with, and the mutants may expand.  When she feels sick again a day or two later and starts to take the antibiotics again, they may not work at all since the resistant mutants have outgrown the other bacteria. She may end up having to get a different antibiotic injected into her bloodstream in the hospital and while she’s there, she may spread the resistant bacteria to other patients.

That’s the story of one mutation giving rise to a bacterial strain resistant against one drug.  The man who passed away in New Zealand was infected with a strain of Klebsiella pneumonia that was resistant against every drug. How did that happen?

The short answer is we don’t know the history of every resistant strain. One interesting example that scientists are following is vancomycin-resistant S. aureus (VRSA). VRSA has been isolated about a dozen times from individual patients.  Most of them were diabetic patients with methicillin-resistant S. aureus (MRSA) infections that coincided with the presence of vancomycin-resistant Enterococcus sp. (VRE).  It’s thought that the VRE transferred its genes for vancomycin resistance to the MRSA, resulting in a strain of S. aureus that is resistant to both methicillin and vancomycin.  This sort of gene transfer can happen inside an infected person or out in the environment.


Scientists are also monitoring how the use of antibiotics in agriculture and aquaculture may promote development of antibiotic resistance.  According to a 2010 review, less than half of all antibiotics are used to treat human infections. Most farm animals are constantly on antibiotics and are known to harbor resistant strains of bacteria, making foodborne illness a potential route to spread resistant bacteria or genes to humans.  To microbiologists, chronic use of antibiotics in agriculture is an obvious route to resistance, but it’s difficult to track exactly where resistant strains originate, so the issue is still controversial.  A study published a few days ago found that MRSA infection rates were statistically correlated with how close Pennsylvania residents lived to livestock feedlots or to fields where swine manure was used as fertilizer.

There is a large gap in our knowledge about the link between antibiotics and agriculture, but it is an active area of research.  Whether you buy antibiotic-free meat or whether you cover your house with Lysol, the one non-controversial and vital thing we can all do is always complete the full course of an antibiotic prescription.


NZs first ‘superbug’ victim? Siouxsi Wiles Nov 2013

The real story behind penicillin. Howard Markel, MD Sept 2013

Antibiotic resistance threats in the United States. The CDC, November 2013

Antibiotic resistance, mutation rates and MRSA. Pray, L. Nature Education, 2008

The emergence of vancomycin-intermediate and vancomycin-resistant Staphylococcus aureus. Appelbaum, P. Clin Micr and Inf Jan 2006

The Origin and Evolution of Antibiotic Resistance. Davies, J. and Davies, D. Microbiol Mol Biol Rev Sept 2010

A call for antibiotics alternatives research. Stanton, T. Trends in Microbiology March 2013

MRSA: Farming up trouble. Mole, B.  Nature July 2013

High-density livestock operations, crop field application of manure, and risk of community-associated methicillin-resistant Staphylococcus aureus infection in Pennsylvania. Casey, JA et. al. JAMA Intern Med Nov 2013

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A closer look at the immune response to DTaP may explain why it wears off

In my last post, I wrote about how the vaccine against whooping cough or pertussis (the “p” in DTaP) may be wearing off.  Scientists are hard at work characterizing the basics of the immune response to the current acelluar vaccine (DTaP) and the formerly prevalent whole bacteria vaccine (DTP).

What exactly does it mean for a vaccine to “wear off”?  Effectiveness is generally measured by how many vaccinated people get sick.  To follow the immune response to a vaccine, scientists measure immunoglobulin (Ig) levels in the blood.  Ig is made by B cells when these cells detect components either made by bacteria or viruses or engineered into vaccines. Among other things, Ig tags bacteria and viruses as a signal for other cells to attack. As the initial immune response downgrades, B cells that make the strongest-binding Ig are stored as memory B cells or as a different form of B cell called a plasma cell.

Memory B cells wait quietly until they see the same microbe and quickly divide and make large amounts of Ig when they do. Plasma cells wait inside bone marrow and constantly release Ig into the blood as an early defense against any re-exposure to a microbe. Measuring Ig over a long period of time is essentially measuring the health and activity of the plasma cells in the bone marrow.  Ig from both types of B cells help neutralize a re-invading pathogen.

Vaccine protection could wane if the vaccine didn’t produce enough memory B cells or plasma cells, or if cells formed but then quickly died off.  So Ig levels, memory B cells and plasma cells have been common benchmarks to study after vaccination.

Kids enrolled in a Dutch study published in September experienced major drops in pertussis-specific Ig two years after their last booster shots.  But this was true for both the whole bacteria and acellular vaccines.

These results are difficult to interpret because the researchers measured Ig responses to the very three proteins engineered into the acellular vaccine.  The whole bacteria vaccine has a lot more than three proteins that B cells can respond to. So even if Ig levels to the three proteins in the study may be lower, the whole cell vaccine could be inducing an overall higher amount of Ig that is just spread over a larger number of proteins and that information could be missed.

By counting memory B cells from in blood samples the scientist also found that kids given either type of vaccine produced some memory B cells that expanded during the first month after booster but dropped back down by the two year time point. Measuring plasma cells in bone marrow is a bit more challenging in human volunteers, but a study published in 2010 tried to compare these cells in mice after giving them DTaP or DTP.

This group actually found more plasma cells in the bone marrow of the DTaP -vaccinated animals. (Again, the issue of only testing the three antigens found in the DTaP may have skewed these results.) They also found poor memory B cell survival and responsiveness to both forms of the vaccine.

The B cells don’t seem to be acting differently in response to the two vaccines. In fact, the current data suggest that B cells do better after the DTaP, so poor B cell responses are unlikely the main culprit behind the vaccine’s waning protection.

Memory T cells are another force to be reckoned with for infectious bacteria like B. pertussis. The same Dutch study that found better long-term pertussis-specific Ig after the acellular vaccine also saw better T cell responses a year after boost with the whole bacteria vaccine.

An in-depth look at the pertussis-specific memory T cells suggested the whole bacteria vaccine may be better at making memory T cells. Instead of making Ig like memory B cells, memory T cells respond to re-exposure to bacteria or viruses by making immune-stimulating proteins called cytokines.  A group of researchers cultured T cells from kids given the acellular or whole cell vaccine with pertussis proteins (again the same three found in the acelluar vaccine).  The T cells made after whole bacteria vaccine responded by making more cytokines than the ones made in response to the acellular vaccine.  These T cells also divided after detecting the pertussis proteins and were twice as likely to make cytokines and divide at the same time.

These are early studies, but it seems that the T cells may be what differentiate the two vaccines.  None of these basic immunology studies followed kids over time to see whether they became infected.  Hopefully this last study will encourage researchers to look for any relationships between T cell responses and long term pertussis immunity.


Differential T- and B-cell responses to pertussis in acellular vaccine-primed versus whole-cell vaccine-primed children 2 years after preschool acellular booster vaccination. SchureRM, et. al. Clin. Vaccin Immunol. Sept, 2013

Impaired long-term maintenance and function of Bordetella pertussis specific B cell memory. Stenger RM, et al. Vaccine. Sept 2010

Different T cell memory in preadolexcents after whole-cell or acellular pertussis vaccination. Smits K, et. al. Vaccine. Oct 2013

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Could whooping cough make another comeback this winter?

Signs outside of Walgreens and CVS have been advertising the flu vaccine for several weeks now.  Even if its effectiveness varies from year to year, I consider it well worth the shot since I work around undergraduates and hospital personnel.  Something I don’t expect to see this winter are advertisements for DTaP (diphtheria, tetanus, acellular pertussis) boosters even though they may be just as important for some as flu shots.

Pertussis, also called whooping cough, is caused by a lung infection with the bacterium Bordetella pertussis. It may sound like a nineteenth century disease you’d catch along the Oregon Trail, but whooping cough is a modern issue and can be serious or fatal, especially for newborns. According to Centers for Disease Control, the last few years have brought the largest pertussis outbreak since the 1950’s, reaching over 50,000 cases in 2012 (compared to a low of about 1000 in 1976).  So, if we have a vaccine, why are there outbreaks?

In the 1950’s widespread use of the DTP vaccine (diphtheria, tetanus, pertussis) began in the U.S. In a couple of decades, the number of whooping cough cases dropped from about 50,000 to fewer than 1000.  The vaccine was effective, but in the late 1970’s and then the 1980’s the vaccine’s side effects took center stage, perhaps as the memory of the disease faded.  The DTP vaccine caused some combination of redness, swelling, pain and fever in about half of the children vaccinated.  Some more serious reactions, like seizures were reported, but were transiently caused by fever and never led to permanent problems.  Concerns that the vaccine caused neurological damage could not be substantiated and throughout the 1980’s, scientists reported that the risk of getting whooping cough outweighed the cost of the side effects.



From our point of view, it may seem brutal to accept such risks, but at the time, DTP was the only option available to prevent a disease that could be much more devastating.  Whooping cough is named after the sound that infants make when they try (sometimes unsuccessfully) to take a breath in between coughing fits.  The infection destroys structures in our lungs called cilia, which are tiny protrusions that collectively brush out grime from our lungs each day.  They are like people in a mosh pit passing unwanted particulates out the door of your airway.  When cilia are disabled, mucus collects in the lungs and your body copes by inducing spastic, uncontrollable coughs.  Some can be extreme enough to slip vertebral discs or break ribs.  The cough can last for months.  For infants, the results are much worse because their lungs and airways are small so they have a much harder time catching their breath.  This story gives an idea of how helpless parents and doctors can be to help an infant with pertussis.

Back to the 1980’s.  Once the fear of the vaccine overcame fear of the disease, a new option had to be explored.  The DTP contained whole bacteria that could not cause infection, but was causing inflammation in many vaccine recipients.  Inflammation occurs when different types of immune cells gather in large numbers and release proteins that expand blood vessels and recruit more immune cells. Swelling follows and the cells release compounds that are meant to damage bacteria, but can also damage tissue.   The process is usually well controlled and only lasts as long as it takes to remove whatever started it all off.  The DTP vaccine, it turned out, caused inflammation because of a type of molecule called endotoxin in bacterial membranes.  Endoxin non-specifically binds and activates immune cells and causes unchecked inflammation.  So work began on a form of the vaccine with individual purified pieces of B. pertussis, called an acellular vaccine. It was approved as a booster by 1991 and the DTaP (diphtheria, tetanus and acellular pertussis) replaced the DTP completely by 1996.

It took about a decade to see the pattern emerge, but it’s starting to become clear that immunity after DTaP immunization does not last as long as immunity conferred by DTP.  Since the vaccine requires 5 boosts, one potential cause could be under-immunization, or a failure to complete the whole vaccine course.  A 2010 study reported that California kids who tested positive for pertussis were less likely to have received a fifth booster, which suggested that a full course was important for protection.  But in the same study, many kids who did get the fifth boost were found in the infected group.   These kids were also more likely to have received the last boost over a year prior to the study. That meant that even after five doses, the vaccine seems to wear off after a year.  A more recent study done in Minnesota and Oregon also showed that kids’ susceptibility to getting pertussis increased a little more each year after the last booster.



So, under-immunization is not the whole story and although the DTaP vaccine works for about a year, there is something fundamentally different between it and DTP.  It’s been suggested that it doesn’t cause enough inflammation or not the right kind of inflammation. So far, there is not enough basic science to support these ideas so researchers are taking a step back to ask simple questions about how the vaccine actually works (More on this in my next post).

Another idea is that B. pertussis is mutating and since DTaP only has a few of the bacteria’s proteins in it, dividing bacteria can start producing fewer or none of those proteins.  This possibility is driving some scientists to explore different vaccine designs with more diverse proteins or to go back to a whole bacteria vaccine (like DTP), but without the super-inflammatory endotoxin.  These explorations will depend on funding and it will take a long time to show that any new vaccine is effective, safe and cost-effective.

In the meantime, parents and doctors have to decide how best to use the existing vaccine to protect kids from whooping cough.  Infants are the most vulnerable to the disease but they can’t be vaccinated for a couple of months after birth.  Doctors and public health officials have turned to boosters for adolescents and adults with the idea that if parents and siblings are protected, they will be less likely to pass the infection to a newborn.

In 2005, the CDC recommended a 6th booster called Tdap for adolescents between 10 and 18 years old.  One study tested the effectives of this method by comparing observed infection rates among infants to rates that were estimated based on data from previous years. They found that actual rates were significantly lower than the projected ones, bringing hope that cocooning may work.  This year, Tdap boosting during pregnancy was deemed safe and was recommended by the CDC.  Hopefully another year or two will bring evidence that vaccinating moms during each pregnancy reduces infant pertussis.

While researchers work on finding a happy medium between the inflammatory whole bacteria DTP and the fair-weather DTaP, we are left with rudimentary options: get Tdap boosters, keep kids up to date on their DTaP doses and wash your hands long enough to sing the “happy birthday” song three times.


“The Pertussis Paradox” Allen, A.  Science Aug 2013

The Immunization Action Coalition


Nature and rates of adverse reactions associated with DTP and DT immunizations in infants and children. Cody, al. Pediatrics Nov 1981

Severe reactions associated with diphtheria-tetanus-pertussis vaccine: detailed study of children with seizures, hypotonic-hyporesponsive episodes, high fevers, and persistent crying. Blumberg, DA et al. Pediatrics Jun 1993

“Pertussis Vaccine: Myths and Realities” Gold, R. Can Fam Physician May 1988

Pertussis and pertussis vaccine: further analysis of benefits, risks and costs. Hinman, AR and Koplan, JP. Dev Biol Stand 1985

Association of childhood pertussis with receipt of 5 doses of pertussis vaccine by time since last vaccine does, California, 2010. Misegades, LK et al. JAMA Nov 2012.

Waning immunity to pertussis following 5 doses of DTaP. Tartof, SY et al. Pediatrics Apr 2013

Tetanus, diphtheria, acellular pertussis vaccine during pregnancy: pregnancy and infant health outcomes. Shakib, JH et al. J Pediatrics Nov 2013.


Getting a better a picture of human immunology

Most of our organs stay in place.  The immune system is different. It moves, it migrates, it ebbs and flows.  Our immune systems are made up of free agent cells that can go to almost any organ and release proteins and compounds that kill viruses, bacteria and infected cells.  Some of these free agents live in the spleen or the lymph nodes.  Some just troll around in the blood looking for pathogens or signals and will go back to these organs or die if they can’t find anything interesting.

There are two kinds of cells that can live a lot longer; even throughout your lifetime.  They start out as B cells or T cells. (B cells come from the bone marrow originally and T cells from the developing thymus.) B and T cells adapt themselves to specific parts of invading viruses and bacteria, so they’re called “adaptive immune cells.”  Some become memory cells after this adaptation, meaning they can respond with a vengeance if they see the same pathogen coming around a second time.  This is the basis for vaccination.


Memory cells need a place to live.  Some live in the spleen and some B cells go back to their roots in the bone marrow to live out their days in peace.  It’s been thought that memory T cells just float around in the body as rouge patrollers and quickly arrive at an organ whenever a repeat offender like the flu rears its ugly head.  But recently, Donna Farber and her lab at Columbia University reported that those reacting memory T cells found at a site of re-infection had been there since the first infection.  They were residents of the lungs and they were very different from the memory T cells in the blood and spleen.

The idea makes sense. The most effective and well-adapted T cells are ready to meet the offending virus on its turf, in this case the lungs. This work, like much immunology, was done in mice, which raises the question, What does this mean for humans, or for vaccine development?  Scientists know so much about the “where and when” features of immune responses because we can pull out any mouse organ at any time and look for any type of cell.  We can count them, classify them, collect them and inject them into another mouse.  You name it, it can be done.

Human immunology, for obvious reasons, can’t be done this way.  Most work done on human immune cells is done with blood samples.  So if memory T cells in organs are fundamentally different from those in the blood, as Dr. Farber’s work suggests, we really only have half the picture.  And it may not even be a very accurate half.

Dr. Farber saw that if we mean to understand the human immune system, our methods have to change.  She initiated a collaboration with the New York Organ Donor Network and her lab has been able to process fresh samples from otherwise healthy brain-dead donors to study the true distribution of immune cells in the human body. The group initially described T cells in the lungs, intestines, spleens, lymph nodes and blood of 24 donors.  The study wasn’t important because of any complicated experiments or newly discovered drug targets, but because it lays out groundwork that has never before been possible.

Biopsy tissues from sick patients (often people with immune diseases) have been the mainstay for immunologists doing human work. The subjects in this study were mostly healthy because they were cleared to be organ donors. The care taken with the tissues and the speed with which they were processed allowed Farber and her group to do more than look at the tissues under a microscope; they were able to culture them and test their functionality. The arrangement also meant that this was the first time multiple tissues taken from the same donor at the same time could be used for immunology studies.

Dr. Farber’s work is providing physicians and immunologists with a picture of the steady state immune system that has never before been available.  And collaborations with other immunology specialists will address other subsets of immune cells in the same tissues. Recently, her group demonstrated that memory T cells against flu live in specific niches along the airways of human and mouse lungs.

The author of a commentary on Farber’s work brought up a 16th century physician named Vesalius, the first to promote post-mortem dissection in a time when the prevailing knowledge of human anatomy was based solely on animal dissection.  Even as our understanding of the mouse immune system grows and becomes more complex, there is huge value in stepping back and defining the basics of the human immune system.

Teijaro J.R., Turner D., Pham Q., Wherry E.J., Lefrancois L. & Farber D.L. (2011). Cutting Edge: Tissue-Retentive Lung Memory CD4 T Cells Mediate Optimal Protection to Respiratory Virus Infection, The Journal of Immunology, 187 (11) 5510-5514. DOI:

Sathaliyawala T., Kubota M., Yudanin N., Turner D., Camp P., Thome J.C., Bickham K., Lerner H., Goldstein M. & Sykes M. & (2013). Distribution and Compartmentalization of Human Circulating and Tissue-Resident Memory T Cell Subsets, Immunity, 38 (1) 187-197. DOI: