General Epidemiology
tsmith | October 27, 2016The 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, from Wikipedia.
It is not, and I think by focusing on the "exoneration" of…
tsmith | September 27, 2016The 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…
tsmith | June 23, 2016[Obvious warning is obvious: potential spoilers for A Song of Ice and Fire novels/Game of Thrones TV series below].
While no one will claim that George R.R. Martin's epic series, "A Song of Ice and Fire," is historically accurate, there are a number of historical parallels that can be drawn from the characters and plotline--particularly from medieval Europe. While most of those relate to epic battles or former monarchs or other royalty, another of Martin's characters, so to speak, is the disease greyscale (1).
Greyscale is a contagious disease that seems to come in at least two distinct forms…
tsmith | May 27, 2016 E. coli, from Wikipedia commons
We've been expecting it, and now it's here.
Yesterday, two article were released showing that MCR-1, the plasmid-associated gene that provides resistance to the antibiotic colistin, has been found in the United States. And not just in one place, but in two distinct cases: a woman with a urinary tract infection (UTI) in Pennsylvania, reported in the journal Antimicrobial Agents and Chemotherapy, and a positive sample taken from a pig's intestine as part of the National Antimicrobial Resistance Monitoring System (NARMS), which tracks…
tsmith | February 1, 2016As you've probably seen, unless you've been living in a cave, Zika virus is the infectious disease topic du jour. From an obscure virus to the newest scare, interest in the virus has skyrocketed just in the past few weeks:
I have a few pieces already on Zika, so I won't repeat myself here. The first is an introductory primer to the virus, answering the basic questions--what is it, where did it come from, what are its symptoms, why is it concerning? The second focuses on Zika's potential risk to pregnant women, and what is currently being advised for them.
I want to be clear, though--…
tsmith | September 10, 2015 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…
tsmith | April 30, 2015I've been working on livestock-associated Staphylococcus aureus and farming now for almost a decade. In that time, work from my lab has shown that, first, the "livestock-associated" strain of methicillin-resistant S. aureus (MRSA) that was found originally in Europe and then in Canada, ST398, is in the United States in pigs and farmers; that it's present here in raw meat products; that "LA" S. aureus can be found not only in the agriculture-intensive Midwest, but also in tiny pig states like Connecticut. With collaborators, we've also shown that ST398 can be found in unexpected places, like…
tsmith | January 15, 2015Measles has come to the happiest place on Earth. As of this writing, a total of 32 cases of measles have been linked to Disneyland visits that took place between December 17th and 20th. About 75% of the cases identified to date were not vaccinated, either because they chose to forgo vaccines or because they were too young, and at least 6 have been hospitalized.
A measles outbreak is a public health disaster, which can cost into the millions of dollars in health resources. You can be sure that public health workers in California and beyond are working overtime trying to identify cases, educate…
tsmith | November 1, 2014I've been asked several times about this NY Post article on the CDC's "admission" that a sneeze could spread Ebola. The Post (which, I should note, is the least credible newspaper in New York City, for those not familiar with the paper) suggests that the CDC has changed their tune regarding the spread of Ebola.
Except, they haven't, and this is a ridiculous, trumped-up non-story, passed along not only by the Post but by others of the typical suspects like conspiracy theorist extraordinaire Mike Adams, aka "The Health Ranger" of Natural News.
Here's what the NY Post claims:
“Droplet spread…
tsmith | October 27, 2014 Left to right, Granny Beck, my Grandma June, and Great-Great Grandma Bertha, circa 1961. Who knows what was on the menu that day.
My Great-Grandpa and Granny Beck were, in some ways, ahead of their time. My Grandpa’s mom and step-dad, they both went through scandalous divorces and then switched partners with another couple, Granny Orpha marrying Wade and my Grandpa’s dad Lee marrying Wade’s ex-wife, Edna. Orpha and Wade raised 5 of Orpha’s boys together, and had a daughter after the divorce/remarriage.
By the time I was born, my Granny Beck was in her 80s, and I have only vague…
tsmith | October 20, 2014The Hot Zone was first released in 1994, the year I graduated high school. Like many readers, that book and Laurie Garrett's The Coming Plague* really sparked my interest in infectious diseases. In some sense, I have those books to thank (or blame?) for my career.
But I'm still going to criticize The Hot Zone, because as a mature infectious disease epidemiologist and a science communicator in the midst of the biggest Ebola outbreak in history, The Hot Zone is now one of the banes of my existence. A recent article noted that the book is back on the bestseller list, going as high as #7 on the…
tsmith | September 23, 2014Have a new article up at Slate. Nine months into the worst-ever Ebola outbreak, here's where we stand.
tsmith | August 8, 2014By the same lead author that published the pig Ebola transmission paper comes a new publication examining airborne transmission among primates. In these, Ebola did *not* spread between non-human primates (NHPs) via air. I sent an email to the PI to comment; will update the post if he responds, but in the meantime, some money quotes directly from the publication:
"One experiment reported contact free transmission between infected NHPs to one uninfected NHP although cross-contamination due to husbandry practices could not be ruled out with certainty26. Interestingly, EBOV infected swine…
tsmith | August 7, 2014Yambuku, Zaire, 1976. A new disease was spreading through the population. Patients were overcome by headaches and bloody diarrhea. The disease was spreading through entire families and wiping them out.
Eight hundred and twenty-five kilometers to the northeast, a similar epidemic was reportedly raging across the border in Maridi, Sudan. Were these outbreaks connected? Despite enormous challenges trying to navigate both the logistics of crossing a landscape of unpaved and unmarked roads, as well as the political difficulties of an attempt to enter and collect samples in an area marked by recent…
tsmith | May 28, 2014After this post on antibiotic resistance, many of you may have seen an exchange on Twitter calling me out for being "knee-jerk" about my call to action to do something about the overuse of antibiotics. In that post, I focused on antibiotic use in agriculture, giving only brief mention to human clinical use. There are a number of reasons for this, and while I didn't discuss them extensively on Twitter, I did want to provide an overview here in order to better explain my position and concern about antibiotic use in agriculture.
How are antibiotics used in animal production?
To start, some…
tsmith | December 4, 2013Regular 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…
tsmith | November 21, 2013Now that seemingly the flu outbreak storyline has been wrapped up on The Walking Dead (unsurprisingly, but disappointingly, with their ineffective treatments proving to be miracle cures), there's still one more zombie microbiology topic I'd like to cover: what's up with the bite, and is it the cause of death? I said previously:
"We know the pathogen can certainly be spread by bites and then cause zombification that way..."
but one commenter disagreed, noting:
"I don’t think we have evidence for that from the show. I think it clearer that zombie bites cause death, and there doesn’t seem to be…
tsmith | November 5, 2013(As previously, spoilers abound)
So on this week's Walking Dead soap opera, we find that Daryl/Michonne's group is still out and about searching for medical supplies. Back at the prison, the food situation is dire (apparently all the food stores were in the cell block where the infection broke out), so Rick and Carol head out to look for both medicines and food from the local 'burbs. During their outing, discussion ensues of Carol's attempt to stop the prison's apparent influenza outbreak by killing two people who, at that point, were the only ones showing symptoms of disease. Rick decides he…
tsmith | October 31, 2013Warning: here be spoilers
In many latter-day zombie movies, books, and TV shows, zombie-ism has a biological cause. In 28 Days Later, the infection is caused by the "Rage" virus, which escaped from a lab when animal rights activists break in and release a group of infected chimpanzees. Of course, one of the animals promptly bites one of its "liberators," and the infection spreads rapidly throughout Great Britain. In Zombieland, it's a mutated form of "mad cow" disease. The Crazies, it's the Trixie virus; World War Z, the Solanum virus; Resident Evil, the T virus. I could go on and on. Zombie…
tsmith | October 28, 2013(Spoilers. And things.)
After the start of season 4 of the Walking Dead and the introduction of a new nemesis: a fast-spreading, deadly infectious disease that seems to be a strain of influenza, I was looking forward to the plot arc of this season.
And then episode 3, "Isolation", happened. From an infectious disease standpoint, I say, bah.
At the end of the previous episode, "Infected", the group had decided to lock up anyone who was showing signs of the infectious disease within the death row cellblock, so that they would not further spread the disease, and to put the children and elderly (…