Rare and Deadly Superbug Mysteriously Appears on U.S. Pig Farms
Not all bacteria are created equal. The first-time discovery of a long-dreaded superbug on U.S. pig farms, announced Monday, really stands out. And not in a good way.
What they found on pig farms was a kind of CRE bacteria, for carbapenem-resistant Enterobacteriaceae. CRE is one of the nastier superbugs. Infections with these germs are very difficult to treat and can be deadly—the death rate from patients with CRE bloodstream infections is up to 50 percent.
The Centers for Disease Control and Prevention (CDC) said these bacteria already cause 9,300 infections and 600 deaths each year. To date, CRE infections occur mostly among patients in hospitals and nursing homes; people on breathing machines or with tubing inserted into their veins or bladders are at higher risk, as are people taking long courses of certain antibiotics. But newer, more resistant kinds of CRE seem to be causing more problems outside hospitals, in communities and among healthier people.
Tom Frieden, head of the CDC, refers to CRE as "nightmare bacteria." Why nightmarish? Because CRE carry genes rendering them resistant to multiple antibiotics—not only to carbapenems, which have been a "last resort" treatment for these kind of infections—but also to other broad spectrum antibiotics, like cephalosporins. CRE have been found on farms before. Monday's report stands out because the carbapenem resistance gene, called bla IMP-27, found on these farms is carried by a plasmid.
Plasmids are strands of DNA that can move easily from one bacterium to another, including across species. After acquiring the right kind of plasmid, with resistance to eight or ten or twelve different antibiotics, a bacterium on a farm or in the human gut could transform from something pretty benign to something lethal in an instant. Previous isolates of CRE found outside of hospitals have been less alarming, because they haven't carried this transmittable plasmid. Earlier this year, scientists also discovered transmissible (plasmid-carried) resistance to colistin—another antibiotic of last resort—in E. coli bacteria isolated from two U.S. pigs.
What happens when—when, not if—the same plasmid collects resistance genes to both colistin and carbapenems? That's the Nightmare on Main Street scenario that many experts fear and perhaps even expect in our future. Infections caused by gram negative bacteria carrying that super-plasmid would be virtually untreatable. As it spreads into the human population, one could reasonably expect a big increase in costs, hospitalizations and deaths.
To some degree, the genie is out of the bottle. By that I mean that farms, like hospitals, are now confirmed as reservoirs of resistance to last-resort drugs, like carbapenems and colistin. Focus now must be on how to change farm practice to try and limit the spread of those superbugs. That's a tall order when it comes to the U.S. pork industry, however.
Today's $22 billion U.S. pork industry may be the perfect storm when it comes to superbug creation. The industry concentrates huge amounts of pigs, manure and antibiotics on relatively few farms in a few counties in a few states. Only 21,687 farms specialize in hog production; they account for 90 percent of hog sales. Just three states, Iowa, North Carolina and Minnesota account for 55 percent of such sales. Routine use of antibiotics on such farms is common (although not carbapenems).
Antibiotic Resistant Infections Kill 23,000 Americans Each Year, Sicken 2 Million https://t.co/cmWhdMiFpF @NRDC @Earthjustice @TEDxManhattan— EcoWatch (@EcoWatch)1481058251.0
Day-old piglets routinely get injected with ceftiofur, which belongs to a critically important human class of antibiotics. Some piglets get multiple doses, increasing the pressure selecting for drug-resistant bacteria in those pigs and on their farms. What's less understood is that using one antibiotic in these settings increases resistance to all the antibiotics that have genes on the same plasmid. CRE bacteria with the bla IMP-27 gene carry resistance not only to carbapenems but also to cephalosporins like ceftiofur. So continuing to use ceftiofur and other antibiotics in weaner pigs likely is a big part of the problem.
Sticking one's head in the sand no longer seems like a viable strategy for the U.S. pork industry. Superbug genes are here and they're on our pig farms. The future's never going to be the same.
David Wallinga, MD, is the senior health officer at the Natural Resources Defense Council.
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After sustained declines in the number of COVID-19 cases over recent months, restrictions are starting to ease across the United States. Numbers of new cases are falling or stable at low numbers in some states, but they are surging in many others. Overall, the U.S. is experiencing a sharp increase in the number of new cases a day, and by late June, had surpassed the peak rate of spread in early April.
Seven day rolling average of number of people confirmed to have COVID-19, per day (not including today). This chart gets updated once per day with data by Johns Hopkins. Johns Hopkins university doesn't provide reliable data for March 12 and March 13. Johns Hopkins CSSE Get the data
To Have a Second Wave, the First Wave Needs to End.<p>A wave of an infection describes a large rise and fall in the number of cases. There isn't a precise epidemiological definition of when a wave begins or ends.</p><p>But with talk of a <a href="https://www.theguardian.com/world/2020/jun/27/new-covid-19-clusters-across-world-spark-fear-of-second-wave" target="_blank">second wave in the news</a>, as an <a href="https://www.american.edu/cas/faculty/mhawkins.cfm" target="_blank">epidemiologist and public health researcher</a>, I think there are two necessary factors that must be met before we can colloquially declare a second wave.</p><p>First, the virus would have to be controlled and transmission brought down to a very low level. That would be the end of the first wave. Then, the virus would need to reappear and result in a large increase in cases and hospitalizations.</p><p>Many countries in <a href="https://doi.org/10.1038/s41562-020-0908-8" target="_blank">Europe and Asia have successfully ended the first wave</a>. <a href="https://www.theguardian.com/world/2020/jun/08/new-zealand-abandons-covid-19-restrictions-after-nation-declared-no-cases" target="_blank">New Zealand</a> and <a href="https://www.newyorker.com/magazine/2020/06/08/how-iceland-beat-the-coronavirus" target="_blank">Iceland</a> have also made it through their first waves and are now essentially coronavirus-free, with very low levels of community transmission and only a handful of active cases currently.</p>
Different States, Different Trends<p>Looking at U.S. numbers as a whole hides what is really going on. Different states are in <a href="https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html" target="_blank">vastly different situations right now</a> and when you look at states individually, four major categories emerge.</p><ol><li>Places where the first wave is ending: States in the Northeast and a few scattered elsewhere experienced large initial spikes but were able to mostly contain the virus and substantially brought down new infections. <a href="https://www.nytimes.com/interactive/2020/us/new-york-coronavirus-cases.html" target="_blank">New York</a> is a good example of this.</li><li>Places still in the first wave: Several states in the South and West – see <a href="https://www.nytimes.com/interactive/2020/us/texas-coronavirus-cases.html" target="_blank">Texas</a> and <a href="https://www.nytimes.com/interactive/2020/us/california-coronavirus-cases.html" target="_blank">California</a> – had some cases early on, but are now seeing massive surges with no sign of slowing down.</li><li>Places in between: Many states were hit early in the first wave, managed to slow it down, but are either at a plateau – like <a href="https://www.nytimes.com/interactive/2020/us/north-dakota-coronavirus-cases.html" target="_blank">North Dakota</a> – or are now seeing steep increases – like <a href="https://www.nytimes.com/interactive/2020/us/oklahoma-coronavirus-cases.html" target="_blank">Oklahoma</a>.</li><li>Places experiencing local second waves: Looking only at a state level, <a href="https://www.nytimes.com/interactive/2020/us/hawaii-coronavirus-cases.html" target="_blank">Hawaii</a>, <a href="https://www.nytimes.com/interactive/2020/us/montana-coronavirus-cases.html" target="_blank">Montana</a> and <a href="https://www.nytimes.com/interactive/2020/us/alaska-coronavirus-cases.html" target="_blank">Alaska</a> could be said to be experiencing second waves. Each state experienced relatively small initial outbreaks and was able to reduce spread to single digits of daily new confirmed cases, but are now all seeing spikes again.</li></ol><p>The trends aren't surprising based on how states have been dealing with reopening. The virus will go wherever there are susceptible people and until the U.S. stops community spread across the entire country, the first wave isn't over.</p>
What Could a Second Wave Look Like?<p>It is possible – though at this point it seems unlikely – that the U.S. could control the virus before a vaccine is developed. If that happens, it would be time to start thinking about a second wave. The question of what it might look like depends in large part on everyone's actions.</p><p>The <a href="https://dx.doi.org/10.1086%2F592454" target="_blank">1918 flu pandemic</a> was characterized by a mild first wave in the winter of 1917-1918 that went away in summer. After restrictions were lifted, people very quickly went back to pre-pandemic life. But a second, deadlier strain came back in fall of 1918 and third in spring of 1919. In total, <a href="https://www.cdc.gov/flu/pandemic-resources/1918-commemoration/1918-pandemic-history.htm" target="_blank">more than 500 million people were infected</a> worldwide and upwards of <a href="https://theconversation.com/compare-the-flu-pandemic-of-1918-and-covid-19-with-caution-the-past-is-not-a-prediction-138895" target="_blank">50 million died</a> over the course of three waves.</p><p>It was the combination of a quick return to normal life and a mutation in the flu's genome that made it more deadly that led to the horrific second and third waves.</p><p>Thankfully, the coronavirus appears to be much more <a href="https://doi.org/10.1016/j.meegid.2020.104351" target="_blank">genetically stable</a> than the influenza virus, and thus less likely to mutate into a more deadly variant. That leaves human behavior as the main risk factor.</p><p>Until a <a href="https://theconversation.com/what-needs-to-go-right-to-get-a-coronavirus-vaccine-in-12-18-months-136816" target="_blank">vaccine or effective treatment is developed</a>, the tried-and-true public health measures of the last months – <a href="https://theconversation.com/this-simple-model-shows-the-importance-of-wearing-masks-and-social-distancing-140423" target="_blank">social distancing,</a> <a href="https://theconversation.com/masks-help-stop-the-spread-of-coronavirus-the-science-is-simple-and-im-one-of-100-experts-urging-governors-to-require-public-mask-wearing-138507" target="_blank">universal mask wearing</a>, frequent hand-washing and avoiding crowded indoor spaces – are the ways to stop the first wave and thwart a second one. And when there are surges like what is happening now in the U.S., further reopening plans need to be put on hold.</p>
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