Vaccine advocacy 101

I recently finished a 2-year stint as an American Society for Microbiology Distinguished Lecturer. It’s an excellent program–ASM pays all travel expenses for lecturers, who speak at ASM Branch meetings throughout the country. I was able to attend Branch meetings from California and Washington in the West, to Massachusetts in the east, and south as far as El Paso, Texas, with many in-between. Each Lecturer selects several topics to speak on, and the Branch chooses from those which they want to hear. Mine included basic research (zoonotic disease, antibiotic resistance) as well as science outreach and advocacy topics (zombies, vaccines).

My talk on vaccines covered vaccine hesitancy and denial, the concerns some parents have regarding vaccination, and the way social media and celebrities contributed to the spread of vaccine misinformation. Inevitably, someone would ask in the Q&A or speak to me afterward inquiring, “But what can I do? I don’t feel I know enough about why people reject vaccines, and feel helpless to combat the fears and misinformation that is out there.” These were audiences of microbiologists and other types of infectious disease specialists–people who are very likely to be educated about vaccines and vaccine-preventable diseases, but who may not have followed the saga of disgraced former physician Andrew Wakefield, or aren’t familiar with the claims of the current anti-vaccine documentary, Vaxxed, or other common anti-vaccine talking points.

To help fill this gap, I recently published a paper in Open Forum Infectious Diseases,” Vaccine Rejection and Hesitancy: a Review and Call to Action.” As the title suggests, in it I give a brief overview of some of the figures in the anti-vax movement and the arguments they commonly use. I don’t go into rebuttals directly within the paper, but the supplemental information includes a subset of both anti-vax literature as well as several published rebuttals to them that interested individuals can look up.

I also briefly review the literature on vaccine hesitancy. Who fears or rejects vaccines, why do they do so, and how might we reach them to change their minds? This is really an area where many individuals, even if they’re educated about vaccines and infectious disease, lack a lot of background. As I note in the paper, many science-minded people still think that it’s enough to just educate people about vaccines properly, and that will be enough. While accurate information is indeed important, for many individuals on the vaccine-hesitant spectrum, it’s not only about misinformation, but also about group identity, previous experience with the health care field, and much more.

Still, vaccine advocates can get involved in a number of way. One of the easiest is simply to discuss your own vaccine history in order to normalize it. I regularly post pictures of my own vaccinations on social media (including my public Facebook and Twitter accounts), and those of my kids*. In over 17 years of parenthood, their vaccinations have all been…boring. These “uneventful vaccination” stories are the ones which rarely get told, as the media focuses on “vaccine injury” stories, in which the injuries may or may not actually be caused by vaccines. Those interested in promoting vaccines can write letters to the editor, get involved with local physicians to speak with hesitant families, break out and be political about vaccine exemptions; there are a number of ways that we can work to encourage vaccination and keep our children and our communities healthy (again, explored in more detail in the manuscript).

Figure 1: Examples of photos posted to the author’s social media accounts. Panel A: The author (middle) and her older children after receipt of seasonal influenza vaccines. Panel B: The author’s youngest child at Walt Disney World, wearing a shirt saying “Fully Vaccinated. You’re Welcome.” Both techniques can serve as conversation-starters around vaccination.

 

I hope this paper will serve as a starting point for those who want to be a vaccine advocate, but just aren’t sure they know enough background, or know where or how to jump in. Whether you’re an expert in the area or not, everyone can do small things to encourage vaccines and demonstrate your trust in them. Those of us working in the area thank you in advance for your help.

Reference:

Smith TCVaccine Rejection and Hesitancy: a Review and Call to Action. Open Forum Infectious Diseases, 2017, in press.

 

*AKA, how to get your kids’ pictures into a scientific paper.

Is there such a thing as an “evolution-proof” drug? (part the third)

A claim that scientists need to quit making:

I’ve written about these types of claims before. The first one–a claim that antimicrobial peptides were essentially “resistance proof,” was proven to be embarrassingly wrong in a laboratory test. Resistance not only evolved, but it evolved independently in almost every instance they tested (using E. coli and Pseudomonas species), taking only 600-700 generations–a relative blip in microbial time. Oops.

A very similar claim made the rounds in 2014, and the newest one is out today–a report of a “super vancomycin” that, as noted above, could be used “without fear of resistance emerging.” (The title of the article literally claims “‘Magical’ antibiotic brings fresh hope to battle against drug resistance”, another claim made in addition to the “no resistance” one in the Scripps press release by senior author Dale Boger). This one claims that, because the modified vancomycin uses 3 different ways to kill the bacteria, “Organisms just can’t simultaneously work to find a way around three independent mechanisms of action. Even if they found a solution to one of those, the organisms would still be killed by the other two.”

A grand claim, but history suggests otherwise. It was argued that bacteria could not evolve resistance to bacteriophage, as the ancient interaction between viruses and their bacterial hosts certainly must have already exploited and overcome any available defense. Now a plethora of resistance mechanisms are known.

Within the paper itself, the limitations are much more clearly laid out. Discussing usage of the antibiotic, the authors note of these conventional semisynthetic vancomycin analogs:

“However, their use against vancomycin-resistant bacteria (e.g., VRE and VRSA), where they are less potent and where only a single and less durable mechanism of action remains operative, likely would more rapidly raise resistance, not only compromising its future use but also, potentially transferring that resistance to other organisms (e.g., MRSA).”

So as they acknowledge, not really so resistance-proof at all–only if they’re used under perfect conditions and without any vancomycin resistance genes already present. What are the odds of that once this drug is released? (Spoiler alert: very low).

Alexander Fleming, who won the 1945 Nobel Prize in Physiology or Medicine, tried to sound the warning that the usefulness of antibiotics would be short-lived as bacteria adapted, but his warnings were (and still are?) largely ignored. There is no “magic bullet;” there are only temporary solutions, and we should have learned by now not to underestimate our bacterial companions.

Part of this post previously published here and here.

HIV’s “Patient Zero” was exonerated long ago

The news over the past 24 hours has exclaimed over and over:

HIV’s Patient Zero Exonerated

How scientists proved the wrong man was blamed for bringing HIV to the U.S.

Researchers Clear “Patient Zero” from AIDS Origin Story

H.I.V. Arrived in the U.S. Long Before ‘Patient Zero’

Gaetan Dugas: “patient zero” not source of HIV/AIDS outbreak, study confirms

HIV’s supposed “Patient Zero” in the U.S., Gaetan Dugas, is off the hook! He wasn’t responsible for our outbreak!

This is presented as new information.

gaetan_dugas
Gaetan Dugas, from Wikipedia.

It is not, and I think by focusing on the “exoneration” of Dugas, a young flight attendant and one of the earliest diagnosed cases of AIDS in the U.S., these articles (referencing a new Nature paper) are missing the true story in this publication–that Dugas was really a victim of Shilts and the media, and remains so, no matter how many times the science evidence has cleared his name.

First, the idea that Dugas served to 1) bring HIV to the U.S. and 2) spark the epidemic and infect enough people early on that most of the initial cases could be traced back to him is simply false. Yes, this was the hypothesis based on some of the very early cases of AIDS, and the narrative promoted in Randy Shilts’s best-selling 1987 book, “And the Band Played On.” But based on the epidemiology of first symptomatic AIDS cases, and later our understanding of the virus behind the syndrome, HIV, we quickly understood that one single person in the late 1970s could not have introduced the virus and spread it rapidly enough to lead to the level of infections we were seeing by the early 1980s. Later understanding of the virus’s African origin and its global spread made the idea of Dugas as the epidemic’s originator in America even more impossible.

When we think of Dugas’s role in the epidemiology of HIV, we could possibly classify him as, at worst, a “super-spreader“–and individual who is responsible for a disproportionate amount of disease transmission. Dugas acknowledged sexual contact with hundreds of individuals between 1979 and 1981–but his numbers were similar to other gay men interviewed, averaging 227 per year (range 10-1560). And while Shilts portrayed Dugas as a purposeful villain, actively and knowingly spreading HIV to his sexual partners, that does not jibe with both our scientific knowledge of HIV/AIDS or with the assistance Dugas provided to scientists studying the epidemic. Dugas worked with researchers to identify as many of his partners as he could (~10% of his estimated 750), as the scientific and medical community struggled to figure out whether AIDS stemmed from a sexually-transmitted infection, as several lines of evidence suggested. There’s no evidence Dugas was maliciously infecting others, though that was the reputation he received. Dugas passed away from complications of AIDS in March of 1984–weeks before the discovery of HIV was announced to the general public.

Furthermore, the information in the new publication is not entirely novel. Molecular analyses carried out in part by Michael Worobey, also an author on the new paper, showed almost a decade ago that Dugas could not have been the true “Patient Zero.” The 2007 paper, “The emergence of HIV/AIDS in the Americas and beyond,” had the same conclusions as the new paper: HIV entered the U.S. from the Caribbean, probably Haiti, and was circulating in the U.S. by the late 1960s–when Dugas was only about 16 years old, and long before his career as a flight attendant traveling internationally. So this 2007 molecular analysis should have been the nail in the coffin of the Dugas-as-Patient-Zero ideas.

But apparently we’ve forgotten that paper, or other work that has followed the evolution of HIV over the 20th century.

What is unique about the new publication is that it included a sample from Dugas himself, via a plasma contribution Dugas donated in 1983, and other samples banked since the late 1970s. The new paper demonstrated that Dugas’s sample is not in any way unique, nor is it a “basal” virus–one of the earliest in the country, from which others would diverge. Instead, it was representative of what was already circulating among others infected with HIV at that time. In supplemental information, the authors also demonstrated how notation for Dugas in scientific notes changed from Patient 057, then to Patient O (for “Outside California”) to Patient 0/”Zero” in the published manuscript–which Shilts then named as Dugas and ran with in his narrative.

patient-zero-graphic
Graphic of sexual network of early AIDS cases, from Auerbach et al., Am J Med 1984.

 

The media then extended Shilts’s ideas, further solidifying the assertion that Dugas was the origin of the U.S. epidemic, and in fact that he was outright evil. The supplemental material notes that Shilts didn’t want the focus of the media campaign initially to be about Dugas, but was convinced by his editor, who suggested the Dugas/Patient Zero narrative would result in more attention than the drier critiques of policy and inaction in response to the AIDS epidemic by the Reagan administration.

And the media certainly talked about it. A 1987 edition of U.S. News and World Report included a dubious quote attributed to Dugas: “‘I’ve got gay cancer,’ the man allegedly told bathhouse patrons after having sex with them. ‘I’m going to die, and so are you.’” NPR’s story adds “The New York Post ran a huge headline declaring “The Man Who Gave Us AIDS. Time magazine jumped in with a story called ‘The Appalling Saga Of Patient Zero.’ And 60 Minutes aired a feature on him. ‘Patient Zero. One of the first cases of AIDS. The first person identified as the major transmitter of the disease,’ host Harry Reasoner said.”

This is the real scandal and lingering tragedy of Dugas. His story was used to stoke fear of HIV-infected individuals, and especially gay men, as predators seeking to take others down with them. His story was used in part to justify criminalization of HIV transmission. So while science has exonerated him again and again, will the public–and the media–finally follow?

 

 

 

 

Just how long does the Ebola virus linger in semen?

The 2013-2016 West African Ebola virus outbreak altered our perception of just what an Ebola outbreak could look like.

While none of the three primary affected countries–Liberia, Sierra Leone, and Guinea-have had a case since April 2016, the outbreak resulted in a total of over 28,000 cases of Ebola virus disease (EVD)–65 times higher than the previous largest EVD outbreak, and more than 15 times the total number of cases of all prior EVD outbreaks combined, from the virus’s discovery in 1976 to a concurrent (but unrelated) outbreak in the Democratic Republic of Congo in 2014.

In March 2016, cases were identified once again in both Liberia and Guinea, just after the outbreak had been declared over. Both countries were declared Ebola-free in June 2016; Guinea for the second time and Liberia for the fourth time. The last series of cases in these countries demonstrated just how different this epidemic was from prior ones, changing what we thought we knew about the virus:

Previous research suggested Ebola could persist in the semen for 40 to 90 days. But that window has been eclipsed in this epidemic by a considerable amount. A probable case of sexual transmission occurred approximately six months after the patient’s initial infection last year in Liberia. Another study found evidence of Ebola in the semen of 25% of surviving men tested seven to nine months after infection. And it takes only a single transmission to kick off a fresh recurrence of the disease.

A recent paper extended this window of virus persistence in the semen even longer–over 500 days. It also explains how the outbreaks began in both countries after being declared Ebola-free–so where did the virus come from?

In a convergence of old-fashioned, “shoe leather” epidemiology/tracing of cases and viral genomics, two converging lines of evidence led to the identification of the same individual: a man who had been confirmed as an EVD case in 2014, and had sexual contact with one of the new cases. Author Nick Loman discussed via email:

The epidemiologists told us independently that they had identified a survivor and we were amazed when we decoded the metadata to find that case was indeed the same person. The sequencing and epidemiology is tightly coordinated via Guinea’s Ministry of Health who ran National Coordination for the Ebola outbreak and the World Health Organisation.

It shows that the genomics and epidemiology works best when working hand-in-hand. If we’d just had the genomics or the epidemiology we’d still have an element of doubt.

The sequencing results also suggested that it was likely that the new viral outbreak was caused by this survivor, and unlikely that the outbreak was due to another “spillover” of the virus from the local animal population, according to author Andrew Rambaut:

If the virus was present in bats and jumped to humans again in 2016, it might be genetically similar to the viruses in the human outbreak but not have any of the mutations that uniquely arose in the human outbreak (it would have its own unique mutations that had arisen in the bat population since the virus that caused human epidemic).

It might be possible that the virus jumped from humans to some animal reservoir in the region and then back to humans in 2016 but because we have the virus sequence from the patients acute disease 15 months earlier we can see that it essentially exactly the same virus. So this makes it certain the virus was persisting in this individual for the period.

So the virus–persisting in the survivor’s semen for at least 531 days–sparked a new wave of cases. Ebola researcher Daniel Bausch noted elsewhere that “The virus does seem to persist longer than we’ve ever recognized before. Sexual transmission still seems to be rare, but the sample size of survivors now is so much larger than we’ve ever had before (maybe 3,000-5,000 sexually active males versus 50-100 for the largest previous outbreak) that we’re picking up rare events.”

And we’re now actively looking for those rare events, too. The Liberia Men’s Health Screening Program already reports detection of Ebola virus in the semen at 565 days following symptoms, suggesting we will need to remain vigilant about survivors in both this and any future EVD epidemics. The challenges are clear–we need to investigate EVD survivors as patients, research participants, and possible viral reservoirs–each of which comes with unique difficulties. By continuing to learn as much as we can from this outbreak, perhaps we can contain future outbreaks more quickly–and prevent others from igniting.

Preparing for the zombie apocalpyse

I have a paper out in the Christmas issue of BMJ on the coming zombie apocalypse.

You read that right. And yes, it was peer-reviewed.

I’ve discussed previously how I’ve used the attention paid to zombies to talk about infectious diseases with children and other audiences; and to bring some science to the Walking Dead and other zombie tales. I even include a zombie lecture as part of the talks I give in my position as an American Society for Microbiology distinguished lecturer.

Why?

Like them or hate them, zombies are part of the zeitgeist. The Walking Dead is still one of the highest-rated programs on television, and its spin-off, Fear the Walking Dead, has been renewed for a second season. Early 2016 will bring us Pride and Prejudice and Zombies on film. Even Aaaahnold Schwarzenegger did a zombie movie. The Girl with all the Gifts was a sleeper hit, and a movie version of the zombie fungus video game The Last of Us is supposedly on the way.

So that’s what the BMJ paper was all about. Of course, it’s ridiculous at its core–no one really expects a zombie outbreak. *But*, we do see new diseases emerging all the time. MERS. Zika virus. Chikungunya. Hendra. Nipah. Pandemic influenza. Other, novel influenzas. And of course, the Ebola virus disease outbreak that is still ongoing in Guinea and Liberia (though cases have finally slowed to a mere trickle).

And we’re still unprepared for them when they become explosive, as Ebola did in 2014. Analyses have showed that the delayed response to that outbreak cost lives. And that’s for a virus that is not particularly easy to transmit, as it’s only spread late in the illness via direct contact with infected bodily fluids. If that had been another virus that was airborne instead of bloodborne, the world could have been in a much worse situation. Now imagine that it was the Solanum virus of World War Z (the book version), slowly incubating in infected individuals as they move all over the globe. Definitely unprepared.

Furthermore, even with our handful of cases in the U.S., we saw that the hype and misinformation about Ebola was out of control. We saw this with H1N1 in 2009 as well, and H5N1 before that. We’re still, as a whole, pretty bad at communicating about infectious disease threats–striking that correct balance of assurance that we know what we’re doing, but acknowledging the gaps in our data and how we’re working to address those. It’s not an easy thing to do, but we need to continue improving. Because again, that’s how it always starts in zombie movies, right?

All-Im-saying-is-Zombie-movie

Ebola and zombies also lead to ethical dilemmas. As I noted in the paper, for a zombie outbreak, there would remain the question of quarantine (for those exposed/bitten but not yet sick), and isolation (for those who are ill)–how would those be handled? What if quarantining the healthy-but-exposed led to essentially a death sentence, as the bitten would inevitably “turn”, and possibly start chowing on the still-living who were quarantined with them? Again, ridiculous on its face, but it has parallels in real-life outbreaks and the legality and ethical quandaries of when to use such measures (and, of course, used with the assumption that they would be effective–which doesn’t always hold). There are accusations that these were violated last year, when individuals coming back from working the Ebola outbreak were quarantined–lacking in scientific justification for sure, and potentially illegal as well.

Using zombies in lieu of real diseases gives researchers, public health professionals, policy makers, and laypeople the ability to discuss these heavy issues without getting bogged down in one specific outbreak or pathogen, because many of the problems we’d face during the zombie apocalypse are similar to those that come up in any serious epidemic: coordination. Funding. Communication. Training. Access to treatment or prevention. Though I didn’t discuss it in this particular article, proper personal protective equipment (PPE) is another issue–both access to it (lacking in developing countries), and being sure to choose the right gear for the outbreak (“overprotection” is not always better). Further, it encourages individuals to put together their own zombie (disaster) preparedness plan, which is how the CDC has used the zombie phenomenon.

In short, it’s way more fun for the average person to shoot the shit about zombies than to have a more serious discussion about influenza, or Ebola, or whatever the infectious disease du jour may be–and maybe even learn a bit of science and policy along the way.

 

Antibiotic resistance: myths and misunderstandings

DSCN2864
A pig flying at the Minnesota state fair. Picture by TCS.

I’ve been involved in a few discussions of late on science-based sites around yon web on antibiotic resistance and agriculture–specifically, the campaign to get fast food giant Subway to stop using meat raised on antibiotics, and a graphic by CommonGround using Animal Health Institute data, suggesting that agricultural animals aren’t an important source of resistant bacteria. Discussing these topics has shown me there’s a lot of misunderstanding of issues in antibiotic resistance, even among those who consider themselves pretty science-savvy.

I think this is partly an issue of, perhaps, hating to agree with one’s “enemy.” Vani Hari, the “Food Babe,” recently also plugged the Subway campaign, perhaps making skeptics now skeptical of the issue of antibiotics and agriculture? Believe me, I am the farthest thing from a “Food Babe” fan and have criticized her many times on my Facebook page, but unlike her ill-advised and unscientific campaigns against things like fake pumpkin flavoring in coffee or “yoga mat” chemicals in Subway bread, this is one issue that actually has scientific support–stopped clocks and all that. Nevertheless, I think some people get bogged down in a lot of exaggeration or misinformation on the topic.

So, some thoughts. Please note that in many cases, my comments will be an over-simplification of a more complex problem, but I’ll try to include nuance when I can (without completely clouding the issue).

First–why is antibiotic resistance an issue?

Since the development of penicillin, we have been in an ongoing “war” with the bacteria that make us ill. Almost as quickly as antibiotics are used, bacteria are capable of developing or acquiring resistance to them. These resistance genes are often present on transmissible pieces of DNA–plasmids, transposons, phage–which allow them to move between bacterial cells, even those of completely different species, and spread that resistance. So, once it emerges, resistance is very difficult to keep under control. As such, much better to work to prevent this emergence, and to provide conditions where resistant bacteria don’t encounter selection pressures to maintain resistance genes (1).

In our 75-ish years of using antibiotics to treat infections, we’ve increasingly found ourselves losing this war. As bacterial species have evolved resistance to our drugs, we keep coming back with either brand-new drugs in different classes of antibiotics, or we’ve made slight tweaks to existing drugs so that they can escape the mechanisms bacteria use to get around them. And they’re killing us. In the US alone, antibiotic-resistant infections cause about 2 million infections per year, and about 23,000 deaths due to these infections–plus tens of thousands of additional deaths from diseases that are complicated by antibiotic-resistant infections. They cost at least $20 billion per year.

But we’re running out of these drugs. And where do the vast majority come from in any case? Other microbes–fungi, other bacterial species–so in some cases, that means there are also pre-existing resistance mechanisms to even new drugs, just waiting to spread. It’s so bad right now that even the WHO has sounded the alarm, warning of the potential for a “post-antibiotic era.”

This is some serious shit.

Where does resistance come from?

Resistant bacteria can be bred anytime an antibiotic is used. As such, researchers in the field tend to focus on two large areas: use of antibiotics in human medicine, and in animal husbandry. Human medicine is probably pretty obvious: humans get drugs to treat infections in hospital and outpatient settings, and in some cases, to protect against infection if a person is exposed to an organism–think of all the prophylactic doses of ciprofloxacin given out after the 2001 anthrax attacks, for example.

In human medicine, there is still much debate about 1) the proper dosing of many types of antibiotics–what is the optimal length of time to take them to ensure a cure, but also reduce the chance of incubating resistant organisms? This is an active area of research; and 2) when it is proper to prescribe antibiotics, period. For instance, ear infections. These cause many sleepless nights for parents, a lot of time off work and school, and many trips to clinics to get checked out. But do all kids who have an ear infection need antibiotics? Probably not. A recent study found that “watchful waiting” as an alternative to immediate prescription of antibiotics worked about as well as drug treatment for nonsevere ear infections in children–one data point among many that antibiotics are probably over-used in human medicine, and particularly for children. So this is one big area of interest and research (among many in human health) when it comes to trying to curb antibiotic use and employ the best practices of “judicious use” of antibiotics.

Another big area of use is agriculture (2). Just as in humans, antibiotics in ag can be used for treatment of sick animals, which is completely justifiable and accepted–but there are many divergences as well. For one, animals are often treated as a herd–if a certain threshold of animals in a population become ill, all will be treated in order to prevent an even worse outbreak of disease in a herd. Two, antibiotics can be, and frequently are, used prophylactically, before any disease is present–for example, at times when the producer historically has seen disease outbreaks in the herd, such as when animals are moved from one place to another (moving baby pigs from a nursery facility to a grower farm, as one example). Third, they can be used for growth promotion purposes–to make animals fatten up to market weight more quickly.  The latter is, by far, the most contentious use, and the “low hanging fruit” that is often targeted for elimination.

From practically the beginning of this practice, there were people who spoke out against it, suggesting it was a bad idea, and that the use of these antibiotics in agriculture could lead to resistance which could affect human health. A pair of publications by Stuart Levy et al. in 1976 demonstrated this was more than a theoretical concern, and that antibiotic-resistant E. coli were indeed generated on farms using antibiotics, and transferred to farmers working there. Since this time, literally thousands of publications on this topic have demonstrated the same thing, examining different exposures, antibiotics, and bacterial species. There’s no doubt, scientifically, that use of antibiotics in agriculture causes the evolution and spread of resistance into human populations.

Why care about antibiotic use in agriculture?

A quick clarification that’s a common point of confusion–I’m not discussing antibiotic *residues* in meat products as a result of antibiotic use in ag (see, for example, the infographic linked above). In theory, antibiotic residues should not be an issue, because all drugs have a withdrawal period that farmers are supposed to adhere to prior to sending animals off to slaughter. These guidelines were developed so that antibiotics will not show up in an animal’s meat or milk. The real issue of concern for public health are the resistant bacteria, which *can* be transmitted via these routes.

Agriculture comes up many times for a few reasons. First, because people have the potential to be exposed to antibiotic-resistant bacteria that originate on farms via food products that they eat or handle. Everybody eats, and even vegetarians aren’t completely protected from antibiotic use on farms (I’ll get into this below). So even if you’re far removed from farmland, you may be exposed to bacteria incubating there via your turkey dinner or hamburger.

Second, because the vast majority of antibiotic use, by weight, occurs on farms–and many of these are the very same antibiotics used in human medicine (penicillins, tetracyclines, macrolides). It’s historically been very difficult to get good numbers on this use, so you may have seen numbers as high as 80% of all antibiotic use in the U.S. occurs on farms. A better number is probably 70% (described here by Politifact), which excludes a type of antibiotic called ionophores–these aren’t used in human medicine (3). So a great deal of selection for resistance is taking place on farms, but has the potential to spread into households across the country–and almost certainly has. Recent studies have demonstrated also that resistant infections transmitted through food don’t always stay in your gut–they can also cause serious urinary tract infections and even sepsis. Studies from my lab and others (4) examining S. aureus have identified livestock as a reservoir for various types of this bacterium–including methicillin-resistant subtypes.

How does antibiotic resistance spread?

In sum–in a lot of different ways. Resistant bacteria, and/or their resistance genes, can enter our environment–our water, our air, our homes via meat products, our schools via asymptomatic colonization of students and teachers–just about anywhere bacteria can go, resistance genes will tag along. Kalliopi Monoyios created this schematic for the above-mentioned paper I wrote earlier this year on livestock-associated Staphyloccocus aureus and its spread, but it really holds for just about any antibiotic-resistant bacterium out there:

And as I noted above, once it’s out there, it’s hard to put the genie back in the bottle. And it can spread in such a multitude of different ways that it complicates tracking of these organisms, and makes it practically impossible to trace farm-origin bacteria back to their host animals. Instead, we have to rely on studies of meat, farmers, water, soil, air, and people living near farms in order to make connections back to these animals.

And this is where even vegetarians aren’t “safe” from these organisms. What happens to much of the manure generated on industrial farms? It’s used as fertilizer on crops, bringing resistant bacteria and resistance genes along with it, as well as into our air when manure is aerosolized (as it is in some, but not all, crop applications) and into our soil and water–and as noted below, antibiotics themselves can also be used in horticulture as well.

So isn’t something being done about this? Why are we bothering with this anymore?

Kind of, but it’s not enough. Scientists and advocates have been trying to do something about this topic since at least 1969, when the UK’s Swann report on the use of Antibiotics in Animal Husbandry and Veterinary Medicine was released. As noted here:

One of its recommendations was that the only antimicrobials that should be permitted as growth promotants in animals were those that were not depended on for therapy in humans or whose use was not likely to lead to resistance to antimicrobials that were important for treating humans.

And some baby steps have been made previously, restricting use of some important types of antibiotics. More recently in the U.S., Federal Guidelines 209 and 213 were adopted in order to reduce the use of what have been deemed “medically-important” antibiotics in the livestock industry. These are a good step forward, but truthfully are only baby steps. They apply only to the use of growth-promotant antibiotics (those for “production use” as noted in the documents), and not other uses including prophylaxis. There also is no mechanism for monitoring or policing individuals who may continue to use these in violation of the guidelines–they have “no teeth.” As such, there’s concern that use for growth promotion will merely be re-labeled as use for prophylaxis.

Further, even now, we still have no data on the breakdown of antibiotic use in different species. We know over 32 million pounds were used in livestock in 2013, but with no clue how much of that was in pigs versus cattle, etc.

We do know that animals can be raised using lower levels of antibiotics. The European Union has not allowed growth promotant antibiotics since 2006. You’ll read different reports of how successful that has been (or not); this NPR article has a balanced review. What’s pretty well agreed-upon is that, to make such a ban successful, you need good regulation and a change in farming practices. Neither of these will be in place in the U.S. when the new guidance mechanisms go into place next year–so will this really benefit public health? Uncertain. We need more.

So this brings me back to Subway (and McDonald’s, and Chipotle, and other giants that have pledged to reduce use of antibiotics in the animals they buy). Whatever large companies do, consumers are demonstrating that they hold cards to push this issue forward–much faster than the FDA has been able to do (remember, it took them 40 freaking years just to get these voluntary guidelines in place). Buying USDA-certified organic or meat labeled “raised without antibiotics” is no 100% guarantee that you’ll have antibiotic-resistant-bacteria-free meat products, unfortunately, because contamination can be introduced during slaughter, packing, or handling–but in on-farm studies of animals, farmers, and farm environment, studies have typically found reduced levels of antibiotic-resistant bacteria on organic/antibiotic-free farms than their “conventional” counterparts (one example here, looking at farms that were transitioning to organic poultry farming).

Nothing is perfect, and biology is messy. Sometimes reducing antibiotic use takes a long time to have an impact, because resistance genes aren’t always quickly lost from a population even when the antibiotics have been removed. Sometimes a change may be seen in the bacteria animals are carrying, but it takes longer for human bacterial populations to change. No one is expecting miracles, or a move to more animals raised antibiotic-free to be a cure-all. And it’s not possible to raise every animal as antibiotic-free in any case; sick animals need to be treated, and even on antibiotic-free farms, there is often some low level of antibiotic use for therapeutic purposes. (These treated animals are then supposed to be marked and cannot be sold as “antibiotic-free”). But reducing the levels of unnecessary antibiotics in animal husbandry, in conjunction with programs promoting judicious use of antibiotics in human health, is a necessary step. We’ve waited too long already to take it.

Footnotes:

(1) Though we know that, in some cases, resistance genes can remain in a population even in the absence of direct selection pressures–or they may be on a cassette with other resistance genes, so by using any one of those selective agents, you’re selecting for maintenance of the entire cassette.

(2) I’ve chosen to focus on use in humans & animal husbandry, but antibiotics are also used in companion animal veterinary medicine and even for aquaculture and horticulture (such as for prevention of disease in fruit trees). The use in these fields is considerably smaller than in human medicine and livestock, but these are also active areas of research and investigation.

(3) This doesn’t necessarily mean they don’t lead to resistance, though. In theory, ionophores can act just like other antibiotics and co-select for resistance genes to other, human-use antibiotics, so their use may still contribute to the antibiotic resistance problem. Studies from my lab and others have shown that the use of zinc, for instance–an antimicrobial metal used as a dietary supplement on some pig farms, can co-select for antibiotic resistance. In our case, for methicillin-resistant S. aureus.

(4) See many more of my publications here, or a Nature profile about some of my work here.

 

The Pap smear is no panacea, Katie Couric

Regular readers keeping up on infectious disease issues might have seen Seth Mnookin’s post yesterday, warning of an upcoming episode of the Katie Couric show  focusing on the HPV vaccine. Even though Mnookin previously spoke with a producer at length regarding this topic, the promo for the show certainly did not look promising:

“The HPV vaccine is considered a life-saving cancer preventer … but is it a potentially deadly dose for girls? Meet a mom who claims her daughter died after getting the HPV vaccine, and hear all sides of the HPV vaccine controversy.”

And indeed, reviews thus far show that unfortunately, Couric pretty much  mangled the issue and allowed heart-wrenching anecdotes to trump science (reminiscent of Jenny McCarthy’s appearance on Oprah). I won’t cover it all (you can view it here), but basically Couric allows stories about illness and death in the weeks following administration of the vaccine to go unchallenged, and brings on Dr. Diane Harper as her HPV expert (featured prominently in the anti-vaccine documentary “The Greater Good“). Dr. Harper believes the HPV vaccine is over-hyped, and that Pap screening is “100% accurate” so no HPV vaccine is really needed. This, frankly, is hogwash. Even with emphasis on screening, here in the U.S. we have 12,000 cases and 4,000 deaths from cervical cancer alone each year. (And in Mnookin’s post and in Matthew Herper’s Forbes post, both note that head and neck cancers can also be caused by HPV as well–but have no good screening process).

Even when HPV cervical infections are caught via screening, the treatment ain’t pretty. I’ve written before mentioning one such remedy–the LEEP procedure.  I had this done several years ago, after a Pap smear came back with abnormal cells and positive for HPV DNA:

“Next, a woman with abnormal cells can expect to undergo a LEEP procedure, where portions of your cervix are removed with a burning electric wire under local anesthetic, and the foul smoking remains of your cells are sucked up into the smoke shark, “a sleek, powerful, smoke-eating machine.” [And one gets to look forward to “coffee ground-like discharge” for up to several days following the procedure, due to the materials they use to stem the bleeding cervix]. After LEEP, side effects may include infection, hemorrhage and possibly cervical incompetence.  These are rare, but if we’re talking vaccine side effects versus possible outcomes from HPV infection, these types of outcomes need to be considered as well–not just death from cervical cancer.”

Being currently pregnant following such a procedure, cervical incompetence was something I was carefully monitored for. Nevertheless, it’s still been a huge source of stress throughout this pregnancy, as this is a significant cause of second-trimester miscarriage and there aren’t great, foolproof ways to detect it, or remedy it if it does occur. Harper acts as if finding HPV via Pap smears is like rainbows and unicorns, but it too has a risk-benefit equation, and I’d so much rather have received a vaccination than to have gone through that. And, some women’s treatments for HPV infections and cervical abnormalities are even more extreme than mine was.

This is why I had my now-almost-14-year-old daughter vaccinated for HPV, and why my pre-teen son will soon be getting his as well. There are multiple ways to prevent HPV-induced cancers, but the vaccine (in combination with routine Pap smears) is by far the least invasive and safest route, as multiple studies have confirmed.

Finally, the show was doubly disappointing because Couric has been such an outspoken advocate of colon cancer prevention, which was the cause of her husband’s death in 1998. While realizing this is a fluff talk show and not the kind of harder journalism she’s apparently now abandoned, she still failed to ask even the most basic of questions to the supposed HPV vaccine “victims” she featured on her show, nor to note during their segments that other possibilities may exist for the girls’ illnesses and death besides the HPV vaccine. In the second segment, Rosemary Mathis even admits blatantly doctor-shopping until one would “listen to her” about her daughter–in other words, give her a new diagnosis (vaccine injury). Why isn’t this even questioned? What did her previous doctors tell her about her daughter’s condition? Couric allowed ratings and anecdotes to trump actual science, potentially causing real harm to the public health. How disappointing that this is now part of her legacy.

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Great editorial response to the Jumbotron ad

The Times Square Jumbotron ad keeps trucking, and with it frustration from the medical and public health community. The American Academy of Pediatrics sent a letter to CBS Outdoors, asking them to pull the ad, to no avail. Rahul Parikh thinks it’s time to do more:

We in medicine need more than letters and passive education for parents on a website. What we really need are some Mad Men of our own. If you want guidance, look at what the folks at the the American Legacy Foundation have done with their anti-smoking campaign, The Truth. Who can forget the TV commercial where a truck pulls up to the headquarters of a tobacco company and teenagers jump out, carrying body bags? We need powerful and unforgettable messages that remind us what’s at stake here.

Have you heard the horrifying whoop of pertussis? Seen how meningitis kills and maims kids, or the painful, paralyzing rigor of every muscle in the body of a child with tetanus? Dear AAP, collect those sights, sounds and the true stories of kids injured by vaccine-preventable diseases and the parents who cried for them when they got sick. Then have the audacity to buy space on a jumbotron, right next to NVIC’s, or in a newspaper the day after Generation Rescue takes out another of its bogus ads. Tell the stories of those parents and children — if they’re still alive today — and make it clear that choosing vaccines means choosing health for kids, families and communities.

I agree with what Parikh is saying, but it’s still sometimes tough to get over my gut reaction to that kind of emotional advertising. He’s right that it can be effective where the simple scientific facts don’t work, but like Chris Mooney notes, it also has to be “presented in a context that doesn’t trigger a defensive, emotional reaction.” For those currently eschewing vaccines for their children, that could be tricky to do, but I wonder how many are true “fence-sitters” and not emotionally committed to an anti-vaccine stance? Those are the ones we really need to work with.

[Edited to add: Steven Novella has a great post up today that reminds us why this is such an important fight: Consequences].

Why are the schools closing and other good H1N1 links…

Over at DailyKos, DemfromCT has an excellent post explaining why it may be beneficial for schools to close temporarily, even if they only have one confirmed case of swine influenza: H1N1: Why Do Schools Close, And When Do They Open?

DarkSyde also has one up on the basic biology and evolution of the flu.

Nick Kristof discusses our lack of attention to public health and what it means in the event of a pandemic in today’s NY Times.

[Updated: and via the comment theads, this post which further discusses what I mentioned here regarding testing–and how the confirmed cases are only the tip of the iceberg (complete with diagram!).