General Epidemiology
tsmith | April 5, 2012The ecology of antibiotic resistance on farms is complicated. Animals receive antibiotic doses in their food and water, for reasons of growth promotion, disease prophylaxis, and treatment. Other chemicals in the environment, such as cleaning products or antimicrobial metals in the feed, may also act as drivers of antibiotic resistance. Antibiotic-resistant organisms may also be present in the environment already, from the air, soil, or manure pits within or near the barns. Ecologically, it's a mess and makes it more difficult to attribute the evolution and spread of resistance to one…
tsmith | March 27, 2012The emergence of "new" diseases is a complicated issue. "New" diseases often just means "new to biomedical science." Viruses like Ebola and HIV were certainly circulating in Africa in animal reservoirs for decades, and probably millenia, before they came to the attention of physicians via human infections. Hantavirus in the American southwest has likely infected many people, causing pneumonia of unknown origin, before the Four Corners outbreak led to the eventual identification of the Sin Nombre virus. Encroachment of humans into new areas can bring them into contact with novel infectious…
tsmith | February 28, 2012Typically when we think of flying things and influenza viruses, the first images that come to mind are wild waterfowl. Waterbirds are reservoirs for an enormous diversity of influenza viruses, and are the ultimate origin of all known flu viruses. In birds, the virus replicates in the intestinal tract, and can be spread to other animals (including humans) via fecal material.
However, a new paper expands a chapter on another family of flying animals within the influenza story: bats.
I've written previously about the enormous diversity of microbes that bats possess. This shouldn't be…
tsmith | February 21, 2012I recently gave a talk to a group here in Iowa City, emphasizing just how frequently we share microbes. It was a noontime talk over a nice lunch, and of course I discussed how basically we humans are hosts to all kinds of organisms, and analysis of our "extended microbiome" shows that we share not only with each other, but also with a large number of other species. We certainly do this with my particular organism of interest, Staphylococcus aureus. There are many reports in the literature showing where humans have apparently spread their strains of S. aureus to their pets (dogs, cats,…
tsmith | November 15, 2011Oh, Discover. You're such a tease. You have Ed and Carl and Razib and Phil and Sean, an (all-male, ahem) cluster of science bloggy goodness. But then you also fawn over HIV deniers Lynn Margulis and Peter Duesberg. Why can't you just stick with the science and keep the denial out?*
But no, now they've let it spill into their esteemed blogs. I was interested to see a new blog pop up there, The Crux, a group blog "on big ideas in science and how these ideas are playing out in the world. The blog is written by an outstanding group of writer/bloggers and scientist/writers who will bring you the…
tsmith | November 9, 2011I've blogged previously on a few U.S. studies which investigated methicillin-resistant Staphylococcus aureus in raw meat products (including chicken, beef, turkey, and pork). This isn't just a casual observation as one who eats food--I follow this area closely as we also have done our own pair of food sampling investigations here in Iowa, and will be doing a much larger, USDA-funded investigation of the issue over the next 5 years.
Let me sum up where the field currently stands. There have been a number of studies looking at S. aureus on raw meat products, carried out both here in North…
tsmith | November 4, 2011I've written a few times about chickenpox parties. The first link refers to a magazine article describing the practice; the second, a few years later, about a Craigslist ad looking to hold such a party "at McDonald [sic] or some place with toys to play on."
Clearly, as chickenpox cases have become more rare in recent decades due to the success of the chickenpox vaccine, moving toward social media to find infections is the way to go. It allows people to find such cases and expose their immunologically naive children to a serious virus, just as easily as googling Jenny McCarthy Body Count."…
tsmith | July 6, 2011While "flesh-eating infections" caused by the group A streptococcus (Streptococcus pyogenes) may grab more headlines today, one hundred and fifty years ago, the best known and most dreaded form of streptococcal infection was scarlet fever. Simply hearing the name of this disease, and knowing that it was present in the community, was enough to strike fear into the hearts of those living in Victorian-era United States and Europe. This disease, even when not deadly, caused large amounts of suffering to those infected. In the worst cases, all of a family's children were killed in a matter of a…
tsmith | June 24, 2011Part One
It appears that the E. coli O104 sproutbreak is starting to wind down, with more than 3,500 cases diagnosed to date and 39 deaths. Though sprouts remain the key source of the bacterium, a recent report also documents that human carriers helped to spread the organism (via H5N1 blog). In this case, it was a food service employee working at a catering company, who spread infection to at least 20 people before she even realized she was infected.
As with many infectious diseases, there are potential lingering sequelae of infection, which can occur weeks to years after the acute…
tsmith | June 23, 2011As I've laid out this week (part 1, part 2, part 3), the realization that a fairly simple, toxin-carrying bacterium could cause a "complex" and mysterious disease like hemolytic uremic syndrome came only with 30 years' of scientific investigation and many false starts and misleading results. Like many of these investigations, the true cause was found due to a combination of hard work, novel ways of thinking, and simple serendipity--being able to connect the dots in a framework where the dots didn't necessarily line up as expected, and removing extraneous dots as necessary. It's not an easy…
tsmith | June 22, 2011I left off yesterday with the initial discovery of "Vero toxin," a toxin produced by E. coli (also called "Shiga toxin" or "Shiga-like toxin"). Though this may initially seem unconnected to hemolytic uremic syndrome (HUS), the discovery of this cytotoxin paved the way for a clearer understanding of the etiology of this syndrome, as well as the mechanisms by which disease progressed. By the early 1980s, several lines of research pointed toward E. coli, and particularly O157:H7, as the main cause of HUS.
A 1982 Centers for Disease Control and Prevention MMWR report found a rare E. coli…
tsmith | June 21, 2011As I mentioned yesterday, the epidemiology of hemolytic uremic syndrome (HUS) was murky for several decades after it was first defined in the literature in 1955. In the ensuing decades, HUS was associated with a number of infectious agents, leading to the general belief that it was a "multifactorial disease"--one that had components of genetics and environment, much like we think of multiple sclerosis today, for example.
Several HUS outbreaks made people think twice about that assumption, and look deeper into a potential infectious cause. A 1966 paper documented the first identified outbreak…
tsmith | June 20, 2011It appears that the E. coli O104 sproutbreak is starting to wind down, with more than 3,500 cases diagnosed to date and 39 deaths. Though sprouts remain the key source of the bacterium, a recent report also documents that human carriers helped to spread the organism (via H5N1 blog). In this case, it was a food service employee working at a catering company, who spread infection to at least 20 people before she even realized she was infected.
As with many infectious diseases, there are potential lingering sequelae of infection, which can occur weeks to years after the acute infection has…
tsmith | June 10, 2011Via H5N1, German officials are calling it for sprouts:
Germany on Friday blamed sprouts for a bacteria outbreak that has left at least 30 dead and some 3,000 ill, and cost farmers across Europe hundreds of millions in lost sales.
"It's the sprouts," Reinhard Burger, the president of the Robert Koch Institute, Germany's national disease centre, told a news conference on the outbreak of enterohaemorrhagic E. coli (EHEC) in northern Germany.
"People who ate sprouts were found to be nine times more likely to have bloody diarrhoea or other signs of EHEC infection than those who did not," he said,…
tsmith | June 9, 2011Maryn McKenna has a great update today on the E. coli situation, looking at where we are as far as unanswered questions about the outbreak and the strain. It's been a messy day; more evidence seems to point to the sprout farm, but CIDRAP also notes that another contaminated cucumber was found in the compost bin of a family sickened by the bacterium (this one had the correct serotype--O104), but it's impossible to tell at this point whether the cucumber was the source of that bacterium or it ended up there from one of the sickened family members. Twists and turns abound in this investigation…
tsmith | June 6, 2011Well, Sunday the said we'd have some results on the sprout tests for E. coli O104:H4. Well, so far the results are negative.
The 1st tests from a north German farm suspected of being the source
of an _E. coli_ [O104:H4] outbreak are negative, officials say. Of 40 samples from the farm being examined, they said 23 tested negative.
Officials had said earlier that bean sprouts produced at the farm in Uelzen, south of Hamburg, were the most likely cause of the outbreak. The outbreak, which began 3 weeks ago and is concentrated in Hamburg, has left 22 people dead. Initially, German officials had…
tsmith | June 5, 2011The E. coli story is moving quickly. A news report out today suggests that sprouts might be the culprit (though it should be emphasized that the outbreak strain hasn't been isolated from these vegetables yet):
Mr Lindemann said epidemiological studies all seemed to point to the plant nursery in Uelzen in the state of Lower Saxony, about 100km (62m) south of Hamburg - though official tests had not yet shown the presence of the bacteria there.
"Further evidence has emerged which points to a plant nursery in Uelzen as the source of the EHEC cases, or at least one of the sources," he said.
"The…
tsmith | June 3, 2011Mike has has a great new post up looking at some molecular analyses of the current European outbreak strain. For anyone who hasn't been paying close attention to what's happening across the pond, there's an ongoing outbreak of enterohemorrhagic E. coli (EHEC)--the type of E. coli that includes O157:H7, which has been associated with outbreaks of disease associated with food. The most infamous outbreak was the 1993 Jack-in-the-Box disaster, associated with undercooked hamburgers contaminated with the organism, but there have also been outbreaks associated with contaminated vegetables (such as…
tsmith | June 3, 2011...when it contains a weird gene conferring methicillin resistance that many tests miss.
Methicillin-resistant Staphylococcus aureus (MRSA) has become a big issue in the past 15 years or so, as it turned up outside of its old haunts (typically hospitals and other medical facilities) and started causing infections--sometimes very serious--in people who haven't been in a hospital before. Typically MRSA is diagnosed using basic old-school microbiology techniques: growing the bacteria on an agar plate, and then testing to see what antibiotics it's resistant to. This can be done in a number of…
tsmith | June 2, 2011At the new blog Puff the Mutant Dragon, there's a great pair of posts looking at the history of plague, with a focus on outbreaks that have occurred here in the US.
Bubonic Plague in America, Part I: LA Outbreak
Bubonic Plague in America, Part II: Undercover Science
I'll also link them in my Black Plague series.