The Long Arm of the Flu Virus

Flu report


Last Friday’s weekly flu report from the Centers for Disease Control (above) told us what we didn’t want to hear:

… that influenza activity is still on the rise overall. In fact, we may be on track to beat some recent records … we could potentially see several more weeks of activity … one out of 10 people who died in the week that has passed died from influenza or pneumonia … these viruses are often linked to more severe illness, especially among children and people age 65 and older.


The link to more severe illness can refer to the onset secondary infections, meaning the virus “opens the floodgates for … bacteria to invade their body,” as happened to this woman with MRSA. An example of this writ large is the influenza pandemic of 1918-1919 (the so-called Spanish Flu) where “the majority of deaths were not caused by the influenza virus.… Instead, most victims succumbed to bacterial pneumonia following influenza virus infection.”

Second, the flu can exhaust healthcare resources allowing superbugs to breach infection control barriers. For example, this month’s VRE outbreak at an Ontario hospital was attributed to the virus:

We had a flood of influenza cases into the hospital and emergency department, and also there were a number of sister institutions that ended up having influenza outbreaks which meant long-term care nursing homes couldn’t take patients, chronic care facilities couldn’t take patients from our hospital so we had a back-up of patients and basically it put a lot of stress on our infection control practices.


The third way the flu virus reaches into our lives is more subtle: we’ll prescribe the wrong treatment for it – namely, an antibiotic – and suffer a severe side effect as a result. For example, the painful and often deadly C. difficile-caused diarrhea; irregular heartbeats and sudden death; tendon rupture; and drug interactions that have people end up in the emergency room.

This is especially so for seniors: As the CBC reports, a recent study found that nearly half of 185,014 Canadians aged 66 or older who go to a family doctor about a cold or other non-bacterial respiratory infection leave with a prescription for an unnecessary antibiotic.

It may sound trite but it’s also true: If you have the cold or flu, antibiotics are not for you. Here’s a chart from the CDC that nicely summarizes things:


ABX relevance 4








What’s a Scientist?

BlackberryMeet Simon Meehan, an engaging 15-year old high school student from County Cork, Ireland, who was just awarded the top prize at the prestigious BT Young Scientist & Technology Exhibition, beating out 1,100 students involved in some 550 projects.

Simon’s interest is in how we can use common plants to treat antibiotic-resistant infections driven by ubiquitous bugs such as Staphylococcus aureus, Methicillin-resistant Staphylococcus aureus (MRSA), and Pseudomonas aeruginosa.

His project is called “Investigation of the antimicrobial effects of both aerial [leaf] and root parts of selected plants against Staphylococcus aureus.” It looked at nine locally sourced plants such as asparagus, nettles and blackberries to test for the presence of chemicals which could potentially be used to control bacterial infection. In the end, he found two plants that did the trick, leaf and fruit extracts from the common blackberry plant (pictured), and a root extract from Mare’s tail. In Simon’s words:

My major conclusion is that I have found an organic non-toxic and locally abundant herb that has antioxidant and antimicrobial effect against MRSA … Staphylococcus aureus, and also Pseudomonas aeruginosa, a potentially deadly bug, especially for those with cystic fibrosis.

I have found an antibiotic that is organic, non-toxic and antimicrobial. And this is in the blackberry of all plants. I mean, you hear of people going to the Amazonian Rainforest, whereas [I] found something outside [my] back door. And I feel, without disrespecting the scientific community too much, there should be some conclusion drawn from this – that we are over-thinking science in too many ways.


Not content to leave it there, Simon wants to extend his research by testing the plant extracts on other bacteria. And he also wants to explore his curious finding that there was “a major difference” in the effectiveness of the blackberry plant depending on the time of year he picked it, June versus August.

Because of Simon’s youthfulness we might conclude that he will be a future force in science. But given what his rigorous research has already uncovered and the further work he has planned, we may want to think about his observation in the video below:

“Science appears to be seen in a much more sophisticated way than necessary. And I feel that we don’t sometimes see what is right in front of our eyes.” (Italics added.)

Mr. Simon Meehan is now waiting on a patent for his extraction method for the blackberry bush that could lead to its widespread use as an antibiotic.


When you use antibiotics you affect the lives of others

The Government of Canada announced this week that farmers – from the small farm to the increasingly prevalent industrial scale “factory farms” – will need a prescription before they can use antibiotics on their food-producing animals. The new rule takes effect this coming December.

Ottawa grounds the need for the rule on:

[T]he emergence of so-called ‘superbugs’ … one of the most significant health threats to Canadians.… [where] The overuse or inappropriate use of antibiotics contributes to the development of [antibiotic resistance] in people and animals. Examples [of inappropriate use] include giving antibiotics to … animals when they are not needed.

Targeting agriculture stops the disease threat at its source. As the chart below demonstrates, bad bugs created on the farm make their way through the environment into your home and community.

Notice the fine print: the use of antibiotics by one person (or group) can adversely affect the health of another person because (1) antibiotics give rise to harder to treat illness and (2) the antibiotics themselves become less effective over time.

No other drug does this. For example, taking aspirin, insulin, or hypertension medication only affects the person taking them and the drugs retain their potency over generations.

Commenting on the government’s new rule and the unique societal feature of antibiotics, John Prescott, retired professor of pathobiology at the University of Guelph, told the CBC that “Farmers need to see this as part of their societal obligation. They need to understand why it’s being done, accept it, embrace it and work with it.”

Prescott notes that it’s not just farmers who have this obligation to others to use antibiotics appropriately: “Everybody has to reduce their use of antibiotics to preserve the effectiveness of antibiotics. This is agriculture stepping up to the plate.” (Emphasis added.)

Livestock 3





A Plea for Plain Language

Tara Smith, PhD, Professor of Epidemiology at the Kent State University College of Public Health.

Tara Smith, PhD, Professor of Epidemiology at the Kent State University College of Public Health.

Be honest. When was the last time you discussed the rising tide of antibiotic-resistant disease, say over coffee at work or over dinner at home?

You know, the issue the World Health Organization says is “a global health crisis … [where] interventions, like organ transplantation, joint replacement, cancer chemotherapy, and care of preterm infants, will become more difficult or even too dangerous to undertake.”

Here’s the thing: It’s not so much that we don’t discuss it – it’s that we can’t discuss it – because we don’t really know what antibiotic resistance means.

That’s what a survey of over 10,000 people conducted by the World Health Organization told us just two years ago: Up to 75% of the people were found to be “confused about this major threat to public health and do not understand how to prevent it from growing.”

So is there a way to engage the public in a conversation about a critical health issue that the majority of us are “confused” about?

Kent State’s Dr. Tara Smith did something refreshingly unique with a paper she published last month – in an open access journal – about the unexpected prevalence of MRSA on public beaches in Ohio. She added this:

Plain Language Summary

Previous studies have examined the presence of the bacterium Staphylococcus aureus on marine beaches, but a rigorous study of freshwater beaches was lacking. We investigated S. aureus presence and proximity to wastewater treatment plants on 10 beaches in Northeast Ohio. We found S. aureus in 22.8% of our samples (64/280). Prevalence was higher in summer than fall. Prevalence was also higher in sites with wastewater treatment plants close to the beaches.


Plain Language/Plain English summaries are making their way into legal reporting too. For instance, the preeminent website for the U.S. Supreme Court is SCOTUSblog. One of its attractions is its Plain English/Cases Made Simple feature. It’s by no means law for dummies: it’s legally reasoned analysis of important cases before the court – without the jargon. For example, in “Wedding Cakes v. Religious Beliefs?: In Plain English,” you’ll find their breakdown of the pending and highly important “cake case” which asks the question, Can a maker of wedding cakes refuse service to a gay couple because of his religious belief that marriage should be limited to opposite-sex couples?

A few years ago in front of a live audience at the Harvard School of Public Health, Stuart Levy, MD, a pioneer in the field of antibiotic-resistant infections, made a rather bold statement. He said that if he had $800,000 to spend on fighting infectious disease, he’d spend $700,000 of it on educating the community because “They need to be a partner in using antibiotics properly.” A co-panelist agreed, saying “We’re all in this together.”

We’re all in this together but unfortunately we’re not all on board. So maybe the thinking of Dr. Levy, and the examples of Dr. Smith and and the U.S. Supreme Court reporters publishing plain language summaries, are worth a serious look.

Because with the ever-increasing presence of genetics (what is the difference between a gene, DNA, and a chromosome?) in science and medicine, this issue will only become more important over time.




Where does disease come from?

Political determinants


The bugs can’t do it alone. For them to cause the greatest possible harm they need our help and unfortunately we seem to be giving it, increasingly so. For example, this month the U.S. Senate refused to extend government health insurance for the nearly 9 million kids and roughly 370,000 pregnant women it protects.

The polite term used in the medical literature for aiding and abetting disease is “the political determinants of health.” The British Medical Journal puts it this way: “Health is a political choice … health is unevenly distributed, many health determinants are dependent on political action, and health is a critical dimension of human rights and citizenship.” (My emphasis.) Thus, if health is a political choice, then so is disease.

Unusual insight into what this means was provided over the weekend in a series of heartfelt tweets (below) from pediatrician Chad Hayes (@chadhayesmd) who practices in rural South Carolina. When you read what Dr. Hayes has to say, keep in mind that it’s well-established in the literature that two other politically-influenced factors, poverty and crowding (e.g., in homes, hospitals, schools, prisons, and shelters) increase the rates of MRSA and other bug-driven infectious disease.

Before I went to medical school, I had little interest in politics. I grew up in a conservative upper-middle class family with two working parents, went to private school for several years, and faced relatively little adversity. (1/x)

I was vaguely aware that there were people who struggled, but rarely encountered them personally. It was children that changed my mind. Not my own, but the ones I care for at work. Kids who, due to a variety of societal problems, aren’t set up for a great future. (2/x)

Today, I woke up yet again in a country where our government has failed to #PutKids1st. We have placed the interests of corporations and the wealthy above those of families who are struggling to survive and children who must strain their eyes to envision a promising future (3/x)

(4/x) It has been over two months since Congress failed to reauthorize CHIP, presumably because the money is needed to fund tax breaks for those who will never have to worry about how to pay their medical bills. We are failing children and putting our nation’s future at risk.

(5/x) I am no longer a conservative. And I am now quite political. And to the politicians who voted for this tax bill, I extend an open invitation to spend my lunch hour in my pediatric office in rural SC, as I struggle to find help for a teen mom with severe depression,

(6/x) a family with 10 people in a single-wide trailer because the house where half of them lived burned down and they have no money to rebuild or replace their belongings, or families where the biggest concern is not whether to contribute to their child’s IRA or college savings,

(7/x) not which private school to use, or which luxury SUV would be the best way to get them there. Their concerns are buying food and infant formula, paying for gas to get to the doctor, and hoping the power company doesn’t shut off their heat this winter.

(8/x) Many are necessarily so concerned about providing for their children today that they have little time, energy, or money to devote to the future. And they are the ones that we are trampling in to minimize the tax burden of people who could lose millions without noticing.

(9/9) I respect that not everyone shares my political views, but for anyone who doesn’t see a problem with this, I’d encourage you to spend some time with the less fortunate. They have changed my perspective, and they may change yours as well. Happy holiday season.

MRSA, PTSD, and Your Family

Eighteen-year-old MRSA survivor Bethany Burke: “These things on my face were taking over. It’s like my face was being invaded. I looked like I had been stung by some venomous insect. They were all over. They were swelling. And it seemed like the more I was taking antibiotics it was like feeding these things on my face. They just kept getting bigger and eventually the one on my eye became so large that I couldn’t open my eye anymore.”



As Sanjay Gupta, MD, reports, Bethany’s ordeal began at age 15 when she developed an irritation on her forehead. After being diagnosed with methicillin-resistant Staphylococcus aureus (MRSA) at a local emergency room, Bethany was treated with several different antibiotics, and the skin abscesses had to be lanced and drained. Health issues related to the infection persisted for the next two years.

“I missed so much school,” says Bethany, then a freshman at Southwestern University in Texas. “Just getting dressed would exhaust me so much that I didn’t have any energy left. While other girls were taking bubble baths, I was checking my body for abscesses and taking diluted bleach baths.”

Although they got the infection under control “it left some pretty deep scars, physically and emotionally,” Bethany says. In fact, she was eventually diagnosed with post-traumatic stress disorder. “Not being able to control what’s going on with your body… nothing makes you feel more helpless.”

And Bethany wasn’t the only one diagnosed with PTSD – so was her mother. “I looked at her and could not believe what I was seeing,” her mother Mary recalls. “The blemish on her forehead was now just enormous. They also spread to her nose and eyelid.”

There’s a saying in the cancer field: when somebody gets cancer, the whole family gets cancer. “Cancer moves in, like a rude and unwanted guest. And, as the patient, you have to understand – as hard as that might be – that it’s not just you alone who has to cope with the disease,” cancer patient Dana Jennings wrote in The New York Times.

It’s easy to see how “MRSA” and “Cancer” are interchangeable in Jennings’ statement, especially since MRSA is contagious. For example, how would you cope when the MRSA patient is your partner with whom you so intimately share living quarters? Or if you’re infected with MRSA and have children, how do you cope with the possibility of infecting them? Or worse, what if, like with the flu, family members started contracting MRSA, one after the other?

A few years ago, the Centers for Disease Control and Prevention conservatively estimated that there are over 80,000 “severe” MRSA infections in the United States each year. However, maybe a better way to understand what the CDC is telling us is this: Each year in the U.S., over 80,000 families are infected with a severe case of MRSA.




The Post-Antibiotic World: “If I need one of these [Antibiotics] down the road is it going to have the effect I need it to? I don’t know the answer to that.”

Screenshot (11)


“If we are not careful, we will soon be in a post-antibiotic era,” said Dr. Tom Frieden, then director of the Centers for Disease Control and Prevention (CDC). “And for some patients and for some microbes, we are already there.”

If you want a glimpse into that post-antibiotic world, take a look at the case of Nicole Scott (pictured above). After a fall she had reconstructive surgery to her left shoulder. The procedure itself went fine but during recovery an excruciating pain set in signaling an infection: “It literally looked like I had a softball sitting on top of my shoulder and I mean I just barely touched it and my shoulder just ruptured,” she said.

Surgery was needed to open and clean the site followed by a night of IV antibiotics. Underneath her skin her doctors found a large pocket of infection that spread from her shoulder to – but not into – her heart.

Weeks later the stitches were removed and the wound was covered till her next follow-up. At the follow-up her bandages were removed and they were shocked to find that the tiny pinpoint hole at the site of the infection had become a hole the size of a quarter – the infection had eaten through the tissue and her skin. That required yet another surgery – and more antibiotics.

The CDC conservatively estimates 2 million such antibiotic-resistant infections in the US alone – every year. Each case will vary in its detail but what happened to Nicole Scott illustrates some of the broad themes: hospitalization, multiple surgeries, pain & disfigurement – and living with the dread of going through it all again.

That dread is what Nicole lives with: Have too many antibiotics taken after her surgery created a harmful tolerance? “If I need one of these down the road is it going to have the effect I need it to? I don’t know the answer to that.”

Nicole Scott is interviewed in this compelling video, which also nicely covers the a, b, c’s of when to use antibiotics. Be sure to click on the full screen icon.


The Responsibility to Protect



Vaccinations protect more people than just those who are vaccinated – they also protect the unvaccinated. Health authorities call this protection “herd immunity” (people around us are referred to as our “herd”). But there’s a catch: there has to be a threshold number of people who get vaccinated before this collective immunity takes effect. Conversely, low levels of herd immunity are often associated with epidemics, such as the measles outbreak in 2014 – 2015 that was traced to exposures at Disneyland in California.

Tara C Smith, PhD, of Kent State, wrote a popular essay this month explaining how vaccination and herd immunity go together. Note that the necessary level of (herd) immunity in the population isn’t the same for every disease:

For measles, a very high level of immunity needs to be maintained to prevent its transmission because the measles virus is possibly the most contagious known organism. If people infected with measles enter a population with no existing immunity to it, they will on average each infect 12 to 18 others. Each of those infections will in turn cause 12 to 18 more, and so on until the number of individuals who are susceptible to the virus but haven’t caught it yet is down to almost zero. The number of people infected by each contagious individual is known as the “basic reproduction number” of a particular microbe (abbreviated R0), and it varies widely among germs.”

For instance, the R0 of pertussis (whooping cough) is 12-17; polio and smallpox 5-7; mumps 4-7; HIV 2-5; influenza, including the 1918 influenza pandemic 2-3; and Ebola 1.5-2.5.

Here’s the thing. If you know how many secondary cases to expect from each infected person, you can figure out the level of herd immunity needed in the population to keep the microbe from spreading. Tara Smith:

This is calculated by taking the reciprocal of R0 and subtracting it from 1. For measles, with an R0 of 12 to 18, you need somewhere between 92 percent (1 – 1/12) and 95 percent (1 – 1/18) of the population to have effective immunity to keep the virus from spreading. For flu, it’s much lower — only around 50 percent. And yet we rarely attain even that level of immunity with vaccination.

Based on that arithmetic, the following table shows what percentage of the population needs to be vaccinated by disease to prevent its outbreak:

R values

Notice that the higher the R0 value, the higher the percentage of people in the community that need to be vaccinated.

Which brings us to the question of who it is that we need to protect – who are the unvaccinated? In general it’s people who are immune-compromised. For example, children who cannot be vaccinated because their immune system is too immature to develop the adaptive immune response that the vaccine is supposed to illicit. Infants who have not yet been vaccinated or have just received a vaccination. The elderly who, because of their age, are often immune-compromised. The sick, whose immune systems can’t withstand the dose of a weakened virus in a vaccine. Those for whom the vaccine didn’t take. And here’s a detailed eye-opening list provided by the CDC that pairs a particular vaccine with health status and warns against vaccination in such cases. All told, we’re talking about a huge swath of people that need protection from infectious disease through herd immunity.

In other words, vaccination campaigns for the flu and other diseases are about much more than individual health. They’re about achieving a collective resistance to disease that involves the whole community.

In the field of international relations there’s a UN doctrine called the Responsibility to Protect. It says that if a nation can’t or won’t protect its own people from harm, then other nations have a right and an obligation to step in and do so. Similarly, on the level of community relations, we know that the very young, the old, and the sick, can’t protect themselves from harm – disease – through vaccination. And so it falls on each one of us to do so: to vaccinate, thereby protecting not just the vulnerable but ourselves and our families at the same time.

Key Vaccination Effect: It greatly reduces the need for antibiotics

We know that vaccines are “incredibly effective” against illness (chart below). Yes, sometimes there are minor short-lived side effects such as swelling at the infection site, but serious side effects are “extremely rare.”

But for those unwilling to vaccinate because of those side-effects, there’s something else to consider that we’ve only recently acknowledged: vaccines reduce the chances that a child will need to be treated with antibiotics. And according to this groundbreaking paper by Alice Callahan about how vaccines reduce our dependence on antibiotics, this matters for three reasons.

Side effects from antibiotics, including diarrhea, rashes and allergic reactions, are generally more common and severe than those from vaccination. “I see far more harm from antibiotics than I do from vaccines, by a huge margin. It’s not subtle,” says one expert.

Second, antibiotics indiscriminately kill bacteria needed for good health, and without them our microbiome  becomes out of balance. Such “dysbiosis” is associated with a number of illnesses including inflammatory bowel disease, multiple sclerosis, diabetes (types 1 and 2), allergies, asthma, autism, and cancer.

And with the good guys out of the way, bacteria that proved resistant to the drugs – the ones that survived – grow and thrive. That makes for more antibiotic-resistant infections, which are harder to treat or which can’t be treated at all.

Take measles as an example. You chose not to vaccinate your child so he or she gets sick. Since measles is bacterial-driven, your child has to take an antibiotic notwithstanding the risks of side effects, upsetting the gut microbiome, and giving rise to drug-resistant bacteria. Further, a measles infection weakens a child’s immune system for up to three years, thus risking further infection and the need for yet more antibiotic treatment.

Perhaps the best example, though, is this vivid illustration of how the pneumococcal vaccine has reduced our dependence on antibiotics. Pneumococcus bacteria can cause pneumonia and invasive blood and brain infections, but it’s also a major cause of ear infections, which are one of the biggest reasons that children are prescribed antibiotics.


Pn vax2


Ideally, says Alice Callahan, we want to protect our kids from deadly bacteria without disturbing the good ones or worsening the trend of antibiotic resistance. And this is exactly what vaccines do. But when parents choose not to vaccinate their kids, they’re increasing the kids’ chances of not only becoming seriously ill, but also of needing antibiotic treatment and other medical interventions down the road.

In other words, vaccines are a tool for decreasing medical interventions.


What Killed Hugh Hefner?


On September 27 this year, Hugh Hefner “died of natural causes at the Playboy Mansion in Las Angeles,” read the headlines announcing his death. And while that’s true, there’s also a deeper story in play that increasingly involves all of us: Antibiotic Resistance – the bugs are beating our drugs.

The way to understand what happened to Mr. Hefner is to look at his death certificate – excerpted above; in full here – and read the four-step chronology that led to his demise like four dominos that fell:

(1) The problem began when Mr. Hefner contracted a strain of E. COLI that was HIGHLY RESISTANT TO ANTIBIOTICS, which led to

(2) A life-threatening bloodstream infection, SEPTICEMIA, where the blood conveys E. coli to bodily organs which the bugs then attack, which led to

(3) RESPIRATORY FAILURE, where the lungs were attacked and succumbed, compromising their ability to move oxygen, resulting in

(4) CARDIAC ARREST, the “immediate cause” of death.

In other words, what drove Mr. Hefner’s death was an antibiotic-resistant E. coli infection that he contracted, the certificate shows, six days before his death. The fact that this strain of E. coli was “Highly resistant” means they threw every drug they had at it yet it beat them all back – that’s antibiotic resistance in action.

It’s crucial to understand that while Mr. Hefner’s age may have factored into why E. coli proliferated in him in the first place – bypassing his body’s natural defenses – his age had nothing to do with why the many antibiotics they gave him didn’t work: that’s a function of the (biochemical) interaction between the bug and the drug.

Earlier this year the World Health Organization published its first ever list of antibiotic-resistant “priority pathogens” – a catalogue of 12 families of bacteria that pose the greatest threat to human health – and E. coli was nowhere to be seen. So as bad as E. coli can be, there’s at least 12 other groups of pathogens out there that are worse (Staph aureus is in the group posing a “High” risk to our health).

There’s one more thing to notice about Mr. Hefner’s death: the only reason we know about the infectious disease component is because California, unlike many states, lists the underlying causes – plural – of a person’s death, i.e., (1) to (3) above. This matters because that’s exactly how infectious disease so often shows its hand – as an initiating factor: but for the infection, there wouldn’t have been a death.

This issue was the focus of a major investigation by Reuters last year, “The Uncounted,” which found that because death certificates are poorly written – asking only for the immediate cause of death – tens of thousands of “superbug” deaths in the U.S. are going uncounted every year.

But that wasn’t the case with Mr. Hefner: His death, like his controversial life, counted.










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