Sunday, March 15, 2020

Pandemic! Not just a game for science nerds.


Unless you've been sequestered somewhere with no internet or newspapers or you've just awoke from a medically induced coma, you've heard there is a virus currently spreading across the planet. I'm adding my voice to the masses that are talking about it. But you love my stories. So, sit back and relax, I mean you're quarantined anyway right? Let me tell you a story about icebergs, exponential growth, flattening the curve, and what preparedness should really look like (hint: it doesn't include hoarding toilet paper). 

Before we dive in, let's learn a little bit. The virus that everybody is talking about right now is called SARS-CoV-2, or Severe Acute Respiratory Syndrome Coronavirus number 2. It causes an illness called COVID-19, or Coronavirus Disease 2019. SARS-CoV-2 and COVID-19 should not be referred to as "China Flu" or "Wuhan virus" or "Wu Flu." If the outlet you are getting your information from has used any of those terms, turn the channel or close your browser window; you are not receiving accurate, helpful COVID-19 information. 

Transmission electron microscope image of SARS-CoV-2; Credit: NIAID RML

There are a whole bunch of coronaviruses out there in the world that infect animals, including humans. There are now seven coronaviruses known to cause disease in humans. Four of them, called the endemic human coronaviruses, are among the viruses that cause the common cold. The other three, SARS-CoV (the first), MERS-CoV, and SARS-CoV-2 are considered highly pathogenic; they can cause severe illness and death. The highly pathogenic coronaviruses are most likely bat viruses that get passed to humans from a different animal. For SARS-CoV it was masked civet cats; for MERS-CoV it's dromedary camels. We're still determining the animal associated with SARS-CoV-2, but do we know the initial outbreak in Wuhan, China is heavily associated with live-animal markets.

The current outbreak of SARS-CoV-2 has been classified as a pandemic by the World Health Organization (WHO). A pandemic is an epidemic that has spread globally. The outbreak first emerged in late December 2019 when health care workers in Wuhan, China noted a marked increase in cases of pneumonia of unknown etiology. That is, pneumonia for which we don't know the cause. At 3:08pm CDT on March 15th, 2020 there are 162,687 cases of COVID-19 reported by cities, states, provinces, counties, and countries across the planet Earth. This is according to a dashboard created by the Johns Hopkins Centers for Systems Science and Engineering. This dashboard is interactive and just a lot of fun...if you're into that sort of thing. Which I am, a lot. The WHO also has a dashboard. What times we live in! Data nerds unite! 

Unfortunately, the COVID-19 numbers are just the tip the iceberg and since the reproductive number is greater than one in a naive population, we're seeing exponential growth. In some places the cumulative number of cases is doubling every day, but thankfully we can see that with measures such as social distancing and testing and isolation we have seen successes in slowing the spread. Okay, okay that was a lot of jargon. Let's learn what it all means.

Tip of the iceberg: 
The iceberg analogy is used frequently when discussing any disease, including infectious diseases. The tip of the iceberg reflects the cases we know about. They have tested positive or are highly suspicious due to illness contact with infected persons or from places where the transmission is occurring. The part of the iceberg we see above the water is much smaller in comparison to the part under the water. There are many people with COVID-19 that we don't know about. They are asymptomatic or have mild illness. Or they were very sick but didn't get tested due to lack of knowledge of care providers, lack of tests, lack of testing reagents, or stringent guidance for who should be tested early on and some places still using that guidance because the system is already overwhelmed.

Credit: Dr. Bhoj R Singh


Reproductive number:
In its purest form, the basic reproductive number (often written as R0 and spoken as R not, which is actually spelled "R naught," because the English language is ridiculous). Anyway. In its purest form, the basic reproductive number is the number of people that any one infected person can go on to infect over the life of their illness, assuming a population with no immunity. It's not necessarily a constant; it can change if the population develops immunity naturally or by vaccination. Or if public health measures slow the spread. During a pandemic like the one we are in now, an R-naught of greater than one means transmission is likely to occur and an R-naught less than one means transmission is less likely to occur. Current research suggests the R-naught for SARS-CoV-2 is greater than one and is, on average, between two and three. Each person with COVID-19 may infect 2-3 people over the course of their illness. Some will infect more; some will infect none.

Exponential growth:
Here's a quick and dirty explanation: case number increases by the number of itself, over time. 8, 16, 32, 64 rather than 4, 5, 6, 7, 8 which is linear. In an epidemic, an important figure related to this growth is called the epidemic doubling time; the time between the doubling of numbers, reported in days for COVID-19. The doubling time is a moving target and is reflective of the situation at any given time and in any given place. The doubling time in China right now is less than that outside of China; the outbreak in China is on the way down and most everywhere else is on the way up. Exponential growth is currently unfettered; it won't stop until everyone is infected, or we have prevention by vaccination or other means. Which brings us to the next point: flattening the curve, community mitigation, and social distancing.

Flattening the curve, community mitigation, and social distancing:
If we're all going to become infected with SARS-CoV-2, let's not all get sick at once. Can we agree? We (collectively as humans) do not have enough ventilators in the world for every person that needs one if they become severely ill with COVID-19 and for those who are already on ventilators due to influenza, cancer, trauma, lung fibrosis, and many other reasons. Let's use the example of panic-buying toilet paper. Each store has a pretty good stock of toilet paper in times of calm. You may have noted on occasion "Why on Earth are there two full rows of toilet paper at this store?" No? Just me? Okay, fine. Normally, even if say 10% of shoppers on any given day are buying toilet paper, there's plenty left on the shelves for the next day and up until the store can restock the shelves. But if 80% of shoppers buy toilet paper at the same time one day, the shelves will be bare, and the store will have to put out everything they have in the stock room. Then the next day, 80% of those shoppers buy toilet paper. Now the shelves are bare and there's nothing in the back. And I'm rationing the three rolls I have left and I had to buy a four pack of cubes of tissues instead the three pack of full packages I usually buy and allergy season has already started. You monsters! I digress. The same thing that will happen in our health care system if we all get sick at once. It's been estimated that around 15% of COVID-19 cases will have severe illness that requires hospitalization and 5% will need intensive care. A portion of the 80% with mild illness may also require hospitalization for pneumonia. We simply do not have enough beds, gloves, gowns, masks, ventilators, dialysis machines, etc. for everyone to get sick all at once. See the "Alert Kitty" below. Flattening the curve is not about making sure our numbers are low in total, it's about spreading them out over time. See the "Lazy Kitty." 

Credit: Dr. Anne Marie Darling

How do we become the lazy kitty? By community mitigation and social distancing. Communities should cancel all large gatherings such as parades, conferences, rallies, concerts, sporting events, schools, etc. You as an individual should avoid crowds, consider doing your grocery shopping online or go to the store when the parking lot is relatively empty. Avoid mass transit if possible or at least try to keep 6 feet between you and the people around you. Wash your hands often and always when you get home from being out in the world. Work from home if that's a possibility. Don't go to work or restaurants or grocery stores if you are sick, even with a cold. Keep your kids home if they are sick. Be a lazy kitty. Help out your elderly and disabled neighbors by offering to shop for them or set them up with a food delivery app if they have a smartphone or tablet. But don't you dare go over there if you are sick or have been exposed to COVID-19. This disease is very deadly for the elderly. Keep them safe.

What preparedness for COVID-19 should actually look like:
  • Make sure you have at least a two-week supply of your prescription and over the counter medications
  • Make sure you have a two-week supply of food and essentials like diapers and toilet paper. TWO WEEKS. Not a supply to last until the end of days. I don’t know how much toilet paper y’all go through in two weeks, but if it requires you to buy 72 rolls, I’m concerned.
  • Create a plan for your family in the event that your household is quarantined or curfews are enacted in your community. This is already happening in the U.S. Hoboken, New Jersey has instituted a curfew from 10pm to 5am, nightly.
And now we come to the portion of the program where we answer viewer questions. I asked my friends and family to give me their burning COVID-19 questions. I've tried to answer to the best of my abilities with the available information. Reminder that this virus is still very new and the answers I found now are subject to change as we learn more.

How long does illness with COVID-19 last? 
  • We don't know for sure. This is a new virus and researchers are working diligently to figure all of this out. 
  • This was the hardest one for me to find an answer for. I've looked at countless journal articles associated with the current outbreak, but almost none have data on time to recovery. What I did found out though is it turns out the "80% have mild illness" figure that we keep seeing out there includes mild pneumonia as well as what I would assume is actual mild illness. So, there's that. Definitely not just "the flu." 
  • I've seen data showing that if pneumonia develops, it's about a week after one starts to feel sick with cough and fever.
  • One case report of an individual with cough and fever who developed mild pneumonia around day 9 of illness that likely was only diagnosed because he was in the hospital (after testing positive, not because he was that sick). This is the first case reported in the U.S. He started to get better on around day 12, but at the time the article was released in late January, he was still hospitalized so we don't know exactly how long his illness lasted in total.
  • One case report of an individual sick with high fever, cough, and fatigue for three days and then recovered. This is a case in Germany that caught COVID-19 from an asymptomatic colleague. 
  • There is a report of 12-32 days from symptom onset to recovery. This is a tiny case study of four medical professionals who all developed mild pneumonia and were treated with antivirals.
  • I have seen modelling studies using a time to recovery of 21-22 days. These are studies that use available data to estimate how an epidemic will play out. And I do remember seeing this 21-day figure in an early report coming out of China, but I can't find the source again. It was looking at hospitalized patients and showed 21 days from onset to recovery and also 21 days from onset to death for those who died.
  • Bottom line: 
    • You'll be sicker longer if you develop pneumonia (be aware of difficulty breathing). 
    • Risk of severe illness requiring hospitalization or of death increases significantly with age over 60 or medical conditions like heart disease, high blood pressure, lung disease, cancer, diabetes, pregnancy (current or recent), kidney, or liver disease.
How long is an infected person contagious?
How does the virus spread (droplet vs airborne)?
  • All available evidence supports that the virus SARS-CoV-2 is spread person to person by respiratory droplets.
  • These respiratory droplets come out of your mouth and nose when you speak or sing or simply breathe and they hang out in the air a little while and then fall. When you sneeze or cough, you expel the droplets much farther. See this great Science Friday video of a sneeze! This is why we keep telling you to sneeze into your sleeve.

  • The virus does not appear to persist in the air like airborne viruses such as the virus that causes measles. That virus is also expelled when coughing or sneezing, but it can remain in the air for up to two hours in its infectious state. A person with measles may sneeze in an elevator and then leave. An hour later, an unvaccinated person enters the elevator and breathes. They are now infected and may go on to develop symptoms. An hour later! There isn't any evidence to support that the virus that causes COVID-19 is spread this way.  
  • Evidence does suggest, however, that the virus can be transmitted by touching inanimate objects or surfaces contaminated with SARS-CoV-2 and then touching your mouth, eyes, or nose.
How long does SARS-CoV-2 live on surfaces?
  • Researchers looked at available data for human coronaviruses (the ones that cause the common cold), the first SARS-CoV, MERS-CoV, and other similar animal viruses. What they found is that human coronaviruses can remain infectious on surfaces for up to 9 days. This varies widely depending on the type of surface (hard vs soft, glass vs metal) and other conditions such as humidity, temperature, and how much virus is present. 
  • These studies are done in laboratories where conditions can be controlled, which is not the case out in the real world.  
  • Don't panic! The studies also show that these viruses are readily removed from surfaces using appropriate disinfectants for the recommended amount of time. More on that next.
What about those wipes by the carts at Target and other stores?
  • Disinfectant wipes and sprays:
  • Check the label where it lists the bacteria, fungi, and viruses that it is active against. Look for human coronavirus or other similar viruses or viruses that are harder to kill than coronaviruses (like Norovirus and other calciviruses). 
  • The EPA has a wonderful list that you can check your product against. https://www.epa.gov/pesticide-registration/list-n-disinfectants-use-against-sars-cov-2
    • Check the label for the EPA Registration number, or EPA Reg. No. and enter that number into the search bar. If your product shows up, it can be used to disinfect SARS-CoV-2. 
    • Follow the instructions for the virus listed in the EPA table and on the label of your product. There will be a specific contact time. This is the amount of time the surface must remain wet in order for disinfection to occur
    • Some products have a very long contact time which can be difficult to achieve. Others, the contact time may only be a few minutes. 
  • Wipes by the carts at Target and other stores:
    • Specifically the blue cart wipes at Target stores in Minnesota: I got lucky the other day at my Target in that I saw a roll of the blue wipes at an empty register waiting to be placed in the cart wipe container (that doesn't tell you what they are or how to use them). The active ingredient of those wipes is 0.12% benzalkonium chloride and that is not on the EPA list of disinfectants to use against SARS-CoV-2. 
    • At other stores or Target if the wipes aren’t blue, check to see if the wipe's product name is on the container. If so, search for it on the EPA website. If not, try to find a manager and ask for the name of the product or the EPA registration number.
    • Consider this though: Will you wait 4 minutes, ensuring the cart handrail remains wet for the whole 4 minutes, before going about your shopping? Did the person before you? Or behind you?  
    • I'm not saying don't use the wipes, they will clean off the boogers and potential fecal matter left by the toddler that was sitting there before you. But they're not really for true disinfection.
What of Africa and other places with low numbers? Why no spread of COVID-19?
  • Wait for it...
    • In Africa, there are outbreaks in South Africa and Algeria and five more countries reported cases on Saturday 3/14/2020
    • In the U.S., as of 4:00pm CDT on 3/15/2020 every state except West Virginia has reported at least one case.
    • Remember the iceberg analogy. 
  • Depending on the capacity to test (kits, reagents, trained personnel), it may be that only the sickest or highest risk or those with obvious links to known cases are being tested.
  • Low numbers do not necessarily mean that there aren’t any cases or that there isn’t any spread.
Why weren't we more prepared in the U.S.?
  • Funding for public health isn't usually a priority when there are so many programs competing for dollars. 
    • Research from the American Public Health Association shows national investment in public health capabilities needs to be around $32 per person and we are, as of October 2019, spending $19 per person.
    • State and local health departments are underfunded and often working with bare bones staffing; this includes public health laboratories.
  • State public health laboratories were required to use the CDC-developed assay and until those labs were up and running, only CDC was doing testing for the entire country.
    • Only those with strong epidemiological connections to the outbreak in China and symptoms of illness were being tested early on. 
    • This no doubt allowed COVID-19 to spread silently. Mild illness usually does not lead one to a doctor's office or hospital. 
    • The first roll out of the test kits included faulty reagents that set testing back by a couple of weeks.
  • Dr. Anthony Fauci said, "The system is not really geared to what we need right now. That's a failing. Let's admit it."
Can I get it from a dog? Do dogs or other pets get infected or spread COVID-19?
  • You may have heard of the dog in Hong Kong that tested positive for COVID-19. The dog's owner had COVID-19 and to be honest, I don't really know why the dog was tested. The original report is behind a paywall. All other reports I've read on veterinary sites state that the dog did not have symptoms of illness.
  • There is no current evidence to suggest that pets play an important role in the spread of COVID-19.
    • However, if you have COVID-19 the recommendation is that someone else care for your pet or service animal. 
    • If that isn't possible, then wash your hands before handling your pet or service animal and avoid snuggling and kissing. 
    • YEAH RIGHT. Sorry Maxdog, if I get COVID-19 you're coming down with me!
Maxdog aka Maxwell Copernicus aka the Best Chihuahua Ever

What am I doing to be safe at work and other places?
  • My coworkers and I in the public health lab and in laboratories all over the world take precautions every day, regardless of COVID-19 or any other infectious disease.
  • We wear gloves, lab coats, and eye protection when in the lab.
  • We only open direct patient samples in a biosafety cabinet that is working properly to keep the air inside the hood.
  • We wash our hands frequently while working in the lab and every time we leave the lab. 
  • I am washing my hands when I come home from being out in the world. I'm not currently doing much else different because, as an introvert, I've been social distancing my whole life! And I have allergies so not touching my face is just not an option. All kidding aside, I do have tickets to a drag show in a couple weeks and I'm keeping a close eye on how things play out. I will follow the guidance of the Minnesota Department of Health and the CDC.
Should I travel?
  • I can't answer this for you. You have to take a number of factors into account.
  • My advice is to pay attention to the CDC's travel website in general, and the COVID-19 page specifically. They have recommendations for international travel, cruises, frequently asked questions, and things to consider for travel within the U.S. https://www.cdc.gov/coronavirus/2019-ncov/travelers/index.html
And last, but certainly not least:
Can I catch COVID-19 while having sex in a hot tub?
  • I know this was a cheeky question, but I'm answering it anyway!
  • Short answer: It depends! Does your partner have COVID-19? Then the answer is yes, you can catch COVID-19 while having sex in a hot tub. Sorry.
  • You're more likely to get "hot tub rash" though, which is a skin infection caused by Pseudomonas aeruginosa. Yuck.
Y'all. I think this is the longest post I've ever done! I mean, it is a pandemic after all, so I guess it's warranted. Let's recap a few key points, shall we?

1. SARS-CoV-2 is the virus that causes an illness called COVID-19.
2. COVID-19 has spread globally, and the WHO has officially called it a pandemic.
3. The virus spreads easily from person to person through close contact and also from touching contaminated surfaces and then touching your mouth, nose, or eyes.
4. Most people who catch COVID-19 will have fever and cough. Some people develop mild pneumonia. Others get very sick and need to be hospitalized. People are dying, particularly the elderly and those with medical conditions.
5. Older age or medical conditions such as heart disease, high blood pressure, lung disease, cancer, diabetes, pregnancy (current or recent), kidney, or liver disease significantly increases your risk of severe illness requiring hospitalization or of death.
6. Nationally and globally, our health care system cannot handle it if we all get sick at once, so we need to practice social distancing.
7. Check on your elderly and disabled neighbors.
8. Wash your hands.
9. Don't hoard toilet paper. Or cold medicine. Or bottled water. Or tissues.
10. Don't have sex in a hot tub. Unless it's your personal hot tub. That no one else ever uses. Then maybe.

Be safe out there. 
World Health Organization: https://www.who.int/emergencies/diseases/novel-coronavirus-2019
Centers for Disease Control and Prevention: https://www.cdc.gov/coronavirus/2019-ncov/index.html



Thursday, June 21, 2018

What's lurking in your veggie tray?

I'll have you know that I was in the middle of writing an epic post, EPIC, about ticks and the diseases they cause when I got distracted by something shiny. Well, not actually shiny. But pink! And fluorescent! So, let's have a little chat about a tiny parasite, eh?

The Minnesota Department of Health sent out a news release recently regarding an increase in cases of cyclosporiasis (sy-klo-spore-I-a-sis) in Minnesota. Cyclosporiasis is a diarrheal infection caused by a parasite called Cyclospora (sy-klo-spore-a) cayetanensis (ky-eh-tan-en-sis). One cluster of infections has been associated with eating at a restaurant in Minneapolis. The other is associated with eating Del Monte vegetable trays containing broccoli, cauliflower, carrots, and dill dip. The Del Monte outbreak is a multistate outbreak, with 144 laboratory-confirmed cases reported so far from Minnesota, Iowa, Wisconsin, and Michigan. Implicated vegetable trays have a "Best If Enjoyed By" date of June 17th. If you're anything like me, this would for sure still be in your fridge where it would remain until eaten, shriveled and limp, or covered in mold. It really just depends on how veggie-hungry I am. Don't be like me; if you have this kind of vegetable tray - THROW IT AWAY. You can read more about this outbreak, including UPC codes of recalled trays on the Centers for Disease Control and Prevention's website here. There is nothing right now to indicate that the two clusters are related. This happens to be the time of year that cyclosporiasis cases increase. I'll explain why later. First, let's get to know our illness-causer.

Cyclospora cayetanensis is an intestinal parasite that can cause watery diarrhea, loss of appetite, weight loss (the "diarrhea diet"), cramping, bloating, increased gas, nausea, and fatigue. Fun stuff. There are other Cyclospora species that can cause similar illness in many different animals. A parasite is a living being that cannot survive on its own; it needs something from another living being. That something can be a place to live, a particular food item, or a blood supply. The parasite typically takes without giving anything in return. Except diarrhea maybe. Not exactly a great relationship. Some parasites are big and can be seen with the naked eye, like ticks. Others are very tiny and can only be seen with the aid of a microscope. Cyclospora is one of the tiny ones. It's just a little bit bigger than a red blood cell measuring 7.5 to 10 micrometers. A micrometer is 1000 times smaller than a millimeter! For you United States customary unit people, 25.4 millimeters is equal to 1 inch. Got it? It's very, very, very small. Here's a Cyclospora selfie:

Microscope image of a Cyclospora oocyst stained with modified acid fast stain.

Pretty, right? This is the view from a microscope at 1000 times magnification (and zoomed in a bit using photo editing software). Okay true talk: Cyclospora doesn't just look like this on its own. We stain it. You put some poop on a clean glass slide, spread it out thinly so that you can read newsprint through it, then let it dry and stain it using a technique called modified acid fast. Pour a type of pink-red stain on the slide and let it sit, rinse with water and remove the pink stain with a kind of alcohol, then pour a type of blue stain on the slide and let it sit, rinse with water and let it dry. Cyclospora has a kind of cell wall that can take up the pink stain and resist being decolorized with the alcohol. We see in the picture above that the background is stained blue. That means the stuff in the background did not take up the pink stain and was decolorized. Instead, the background stuff took up the blue stain. Most of that blue stuff is bacteria! This is a smear of poop after all. And poop is LOADED with bacteria. Trust me. The ruler that is across our Cyclospora is used to measure things under the microscope. Each hash line is one micrometer. The oocyst (O-O-sist) here measures 9 micrometers. What is an oocyst you ask? Let us learn.

This is a representation of Cyclospora's life cycle that I shamelessly stole from CDC's website. Start at number 1 below.

Image of the Cyclospora life cycle.
We begin with an unsporulated oocyst in the environment. Think of this like an unfertilized egg. More on environment later.

Days to weeks pass at temperatures ranging between around 22 to 32 degrees Celsius, equivalent to 71.6 to 89.6 degrees Fahrenheit (come on America, get with the metric system!!).

At the optimal time and temperature for each oocyst, sporulation occurs. What happens is there a division within the oocyst from one sporont into two sporocysts. This sporulated oocyst is infective; it can make you sick if you ingest it.

How might you ingest this oocyst? When the unsporulated oocysts are deposited on food that is meant to be eaten fresh such as cilantro, basil, or berries or if the oocysts end up in the water supply, and they sporulate and become infective, then humans can swallow them and become sick.

Inside of the human gut, Cyclospora continues its life cycle. The oocyst breaks open and releases the two sporocysts which in turn release tiny wormy things called sporozoites.

Dissecting microscope image of a broken open Cyclospora oocyst with one sporocyst outside of the cell and one inside the cell.
Picture of Cyclospora oocyst releasing a sporocyst courtesy of CDC DPDx

The sporozoites invade the epithelial cells of the small intestine. These cells are kind of like your outer skin cells, except they are inside your body. It's this invasion of your cells that causes the symptoms I listed above. Many symptoms of infectious diseases are due to your body trying to rid itself of the offending thing. The sporozoites multiply inside your small intestine cells and mature into oocysts which are then passed in your poop.

When you get sick with Cyclospora and have watery diarrhea you are shedding the unsporulated oocysts. This is good in one way; the unsporulated oocysts are not infective. There is no direct human to human transmission of Cyclospora. There needs to be some time and the right temperature that we talked about earlier in order for Cyclospora to become infective. It's this unsporulated oocyst found in poop that we can identify in the laboratory.

Laboratories can make a smear and perform the modified acid-fast stain that I described above. This is relatively easy, and we can view the slide under a regular light microscope that most laboratories have access to. Another cool thing about Cyclospora, you know other than its pinkness, is that it's fluorescent! All by itself! If we place a drop of poop onto a glass slide and look at it under a fancy fluorescent microscope, we can look for small round objects that glow pale blue. (Note: you do have to use the right filter on the microscope in order to "excite" this wavelength of color. For you nerds out there, it's a 330-365nm ultraviolet excitation filter.)

Microscope image showing a single fluorescent Cyclospora oocyst in a stool sample.

In the middle of the picture above we see a round blue object amidst a bunch of yellow-orange junk. Again, much of that junk is bacteria. This picture really doesn't do it justice. It's really neat!
Below, we see another view of the same poop sample. How many oocysts can you find? I'll show you at the end of this post.

Microscope image showing fluorescent Cyclospora oocysts in a stool sample.

So far, we've learned that Cyclospora is a tiny parasite that can make us sick if we eat contaminated food or drink contaminated water. Often, the kinds of foods that can become contaminated with Cyclospora are fresh produce items like raspberries, basil, cilantro, and others. How does the food or water become contaminated in the first place? This is a question that is sometimes hard to answer and sometimes very, very easy to answer. The short story is that the food or drink somehow comes into contact with the poop of a sick person or persons. The long story can be very complicated and many times when cyclosporiasis cases are found, exactly how it happened is never fully understood. Let me tell you about a whole bunch of cyclosporiasis cases and the outcome that I can't get out of my mind.

Every year beginning around April or May, the United States sees an increase in cases of cyclosporiasis reported to health departments across the country. This increase coincides with warmer weather and the abundant availability of fresh produce that occurs in the summer months. This is not to say that produce grown within the United States is the culprit. People who get sick with cyclosporiasis have eaten food while on vacation or have eaten contaminated food that was imported for sale in the United States. When a case of cyclosporiasis is reported to a health department, the person is contacted, and health department officials ask questions about food eaten in the days and weeks leading up to the onset of illness. When there are multiple cases and similarities in food eaten are found, health department officials start to ask more specific questions. Where did you buy those raspberries? What restaurant did you go to where you ate that salad? If most of the people who are sick say that they ate salads at restaurant A, then the health department will talk to the folks at restaurant A. Where do you get your lettuce? How about garnishes, cilantro specifically? These were likely the kinds of questions being asked during the cyclosporiasis outbreaks of 2012, 2013, and 2014. The Food and Drug Administration (FDA) does also get involved in these investigations which are called "traceback" investigations. So-called because we're trying to trace back from the sick person to find what made them sick and where it came from so that we can fix whatever problem is happening and prevent more illnesses. Some of those outbreaks in 2012 through 2014 led officials to fresh cilantro that was imported from an area of east-central Mexico. Then it started happening again in 2015. I don't know all the details of the investigations and I certainly don't know why it took so long to reach the conclusion that was ultimately reached. You can read about it on the CDC's website and also in this FDA import alert. Pay close attention to paragraph six under "Reason for alert." FDA and Mexican regulatory authorities went to check out the farms and packing facilities that the traceback investigations led them to. They "inspected 11 farms and packing houses that produce cilantro in the state of Puebla, 5 of them linked to the US C. cayetanensis illnesses, and observed objectionable conditions at 8 of them, including all five of the firms linked through traceback to the U.S. illnesses. Conditions observed at multiple such firms in the state of Puebla included human feces and toilet paper found in growing fields and around facilities; inadequately maintained and supplied toilet and hand washing facilities (no soap, no toilet paper, no running water, no paper towels) or a complete lack of toilet and hand washing facilities; food-contact surfaces (such as plastic crates used to transport cilantro or tables where cilantro was cut and bundled) visibly dirty and not washed; and water used for purposes such as washing cilantro vulnerable to contamination from sewage/septic systems. In addition, at one such firm, water in a holding tank used to provide water to employees to wash their hands at the bathrooms was found to be positive for C. cayetanensis."

Ewwwww. 😲

There. Now you'll have that story stuck in your head too. But you know what? I still eat fresh produce and you should too! Because it's delicious and good for you and the likelihood of getting cyclosporiasis from eating fresh produce is very slim.

So, what can you do? I don't have handy list for you! Unfortunately, there's not a ton that you can do for prevention. CDC recommends following safe fruit and vegetable handing recommendations, which is all well and good. However, Cyclospora isn't easily washed off of fruits and veggies and it's resistant to many disinfectants and sanitizing methods. You can wash your produce and keep it in the refrigerator. Remember, Cyclospora needs to be at warm temperatures in order to mature into the form that can make people sick. You can make an effort to buy produce that is grown locally: frequent your local farmer's market or join a CSA. If you do happen to get sick with cyclosporiasis, don't prepare food for others, wash your hands frequently, and don't go to public pools. You are shedding many Cyclospora oocysts! Here's the picture from above where I asked how many oocysts you could find.


I counted five! Consider that this is just one view of one microscopic field in one drop of poop. The volume of poop expelled during a diarrheal event can be significant. I can't even do the math to figure out how many oocysts would be found in your toilet.

The Del Monte outbreak is growing rapidly. When I started writing this post on the 19th, there were 78 reported cases. As of today, the 21st, there are almost twice that many. Six people so far have been hospitalized. Hospitalizations are often due to critical dehydration from the watery diarrhea. If left untreated, symptoms of cyclosporiasis can last for weeks or months. Diarrhea can go away and come back. The treatment for cyclosporiasis is an antibiotic, but if you are allergic to "sulfa" drugs you can't take it. If you have a healthy immune system though, you can recover without treatment. Take care of yourself if you're sick! And throw away those veggie trays if they're still in your fridge. Be safe out there!







Wednesday, October 18, 2017

Don't be lame. Get your flu shot.

I'm getting a little tired of hearing this: "I got the flu once after getting the shot, I'll never get it again." No, you didn't.

WARNING: RANT AHEAD
Also, at what point did your primary care provider become "government" or in the pocket of Big Pharma? The recommendation to get your flu shot if you are able is not some government conspiracy or ploy for pharmaceutical companies to make oodles of money. Guess what? Your doctor doesn't work for the government and pharmaceutical companies make more money on erectile dysfunction and high blood pressure medications than they ever will on a once-a-year vaccine. You may think it's not a big deal if you don't get your flu shot because you're reasonably healthy and it's okay if you get sick for a week. That may very well be true. But consider your grandparents, parents of a certain age, and babies and other young ones. Consider your friend or family member or acquaintance or stranger on the bus that may be immunocompromised due to cancer treatments. Cancer is BAD ENOUGH without having to worry about catching influenza from someone that just doesn't "believe in vaccination," like getting vaccinated is on the same level as believing in leprechauns. Consider what it means to miss an entire week of work. I came down with influenza last year, two weeks before my work had its flu shot event. It was awful. Body aches so intense that the weight of my own body was almost too much to bear. Fever spikes up to 103 degrees. I never want to go through that again. You shouldn't be so flippant about it. 
END RANT

Here are some flu facts:

Fact: Influenza kills. Over a period of 30 years between 1976 and 2006, estimates of flu-associated deaths in the United States range from a low of about 3,000 to a high of about 49,000 people per season. During a regular flu season, around 90 percent of deaths occur in people 65 years and older. Children die too; 107 children under age 18 died from influenza during the 2016-17 season. These deaths very well could have been prevented by vaccination. A study conducted by the Centers for Disease Control and Prevention (CDC) showed that between 2010 and 2014, of 291 deaths in children 6 months to 17 years, only 26% had been vaccinated against flu before getting sick. We can do better for our kids. We can do better for our parents and grandparents.

Fact: You cannot get the flu from the flu shot. Flu shots are made either from a dead virus or with no virus at all, depending on which shot you get; it's biologically impossible for the flu shot to give you influenza.

Fact: The shot itself and what your body does to make the antibodies that protect you can cause body aches and possibly a low-grade fever. Don't be a wuss, that's not influenza.

Fact: It can take up to 2 weeks after getting the shot for your body to do what it needs to protect you. So, you could potentially have come in contact with influenza before you got the shot, or sometime in that 2-week window, and still get sick. 

Fact: The flu mist (nasal spray) is made with live virus, but one that's had its nastiness factors taken away. You may have more localized side effects like runny nose, cough, or sore throat, but the flu mist cannot give you full-blown influenza. Not possible.
         Sub-fact: The flu mist is NOT available this year and I don't know when or if it will be back. 

Fact: The "stomach flu" is not influenza. It's most likely a nasty little bugger called norovirus. I'll talk about that fresh hell another day. Stop calling it the flu.

Here's the thing. I'm not going to lie to you; the flu shot isn't perfect, it won't protect everyone and for some it won't work at all. But it is the best we have and we have to do the best we can with what we have! The recommendation is everyone age 6 months and older that is able should get their flu shot. It's the right thing to do for the herd! Plus, this year's flu season could potentially be a real doozy. We can often look to the southern hemisphere for a clue of how things will go for us. Australia is just entering their spring season and the flu season is winding down. And it was bad. Here's a news article from the country outlining the severity. 


To re-cap: Your primary care provider does actually look out for your best interests. The flu shot won't give you the flu. It will help to protect you and the people around you. Most people age 6 months and older can get the flu shot. Talk to your health care provider to make sure you are able. Do your part and get vaccinated!! Don’t be lame.

Sunday, August 6, 2017

When good bacteria go bad: Shiga toxin-producing Escherichia coli

Two young children, siblings - brother and little sister, got sick last month. The little girl sadly succumbed and passed away. Her older brother was gravely ill, fighting for his life, slowly recovered, and is now thankfully home. What could have caused this unfathomable tragedy? A strain of normally beneficial bacteria, Escherichia coli, or E. coli (E-coal-I).

E. coli is a kind of bacteria that lives in the guts of mammals, including humans, cows, sheep, and goats. Garden variety E. coli doesn't cause any harm, maybe a little gas. Sometimes it ends up in your urethra and causes a urinary tract infection. No big deal (unless it's resistant to antibiotics, but we've gone there already). Unfortunately, there also exist pathogenic E. coli. These are the strains of E. coli that can make us sick. You can think of different strains of a certain bacteria as flavors of ice cream. Vanilla, chocolate, mint chocolate chip, Rocky Road, whatever you like. It's all ice cream (E. coli), but it comes in many different flavors (strains). There are strains of E. coli that are sticky and adhere to the lining of your intestines more than others. Some of those sticky strains also can cause you to have diarrhea, and a lot of it. As your intestines become a mad torrent of watery contents, many of your normal beneficial bacteria are swept away in the tide. The E. coli strains that are more sticky are able to hang on tight. Then once the rest of your bacteria are gone, they can take over the area without any competition. There are several different groupings of pathogenic E. coli and to talk about them there's going to be a lot of long words that are hard to pronounce and lots of abbreviations. Hang on tight. First thing to note: the prefix "entero" refers to the intestine. 

Enterotoxigenic E. coli, or ETEC,
Enteropathogenic E. coli, or EPEC,
Enteroaggregative E. coli, or EAEC,
Enteroinvasive E. coli, or EIEC,
Diffusely adherent E. coli, or DAEC,
and Shiga toxin-producing E. coli, or STEC. Also known as Enterohemorrhagic (EHEC), or Verocytotoxin-producing (VTEC). 

The groups listed above all have varying abilities to stick to your intestinal wall, to resist your stomach acids, and to cause you to have diarrhea that can be bloody. STEC (S-teck) is what you hear about in the news, mostly when there is an outbreak of illness caused by contaminated food. STEC is a bad guy, a really bad, bad bacteria. STEC is what we're talking about here. 

The kind of STEC that you've probably heard of is called E. coli O157:H7, sometimes referred to as E. coli O157 or simply as O157. The "O" number refers to an antigen on the surface of the bacterial cell wall. The "H" number is an antigen on the flagella (whip-like appendages that allow the bacteria to swim around). I don't want to get too into the weeds about bacterial cell wall structures and whatnot. What's important is there is tremendous variability of "O" and "H" antigens among bacteria like E. coli and so we use them in microbiology to separate, categorize, and name. This is called serotyping. E. coli O157:H7 is a serotype of STEC. There are many other serotypes of STEC besides O157. We have O111, O26, O104, O121, and O145 to name a handful; there are a lot more. Last year there was a multi-state outbreak of STEC infections caused by O121 and O26 that was associated with consuming raw flour, like eating undercooked baked goods or pizza dough, or licking the spoon when you make cookies. In 2011, there was a massive outbreak of STEC infections caused by O104:H4 associated with eating contaminated raw fenugreek sprouts: 4,075 cases and 50 deaths in 16 countries.

Why does STEC cause so many illnesses? Why do people get so sick? STEC produces toxins called Shiga toxins, named after Dr. Kiyoshi Shiga - the doctor who discovered the bacteria responsible for dysentery. Those of you old enough, and young enough, and Minnesotan enough, to have played the game Oregon Trail may recall members of your caravan dying of dysentery on the long journey west. 
(Image: MECC)

Dysentery is a diarrheal illness caused by bacteria called Shigella which are very similar to E. coli, and produce the same kind of toxin. 80 years after the discovery of the Shiga toxin that causes dysentery, researchers discovered the toxins in certain strains of E. coli, the STECs. Shiga toxins are toxic to the kinds of cells that line the intestines, causing damage to the lining. In the grand scheme of things, having a damaged intestinal wall doesn't seem all that terrible. You'll probably have a "stomach ache" and some diarrhea, albeit bloody which is not awesome. But you'll probably get better in a few days and be back to somewhat normal. But remember I said the STECs are the really bad guys. Sometimes an infection with STEC can lead to a complication called hemolytic uremic syndrome, or HUS. 

HUS is a disease that involves the kidneys, red blood cells, and platelets (cells that clot your blood). It most often affects young children and can cause severe illness and death. The two siblings I told you about at the beginning both developed HUS. This disease can also be caused by other bacterial infections, some viruses, medications, and other reasons. HUS occurs in about 5-10% of STEC infections. 

Somehow (researchers are still working this out), the toxins get out of the intestines where they are drawn to cells that produce what are called Gb3 receptors. A receptor is defined as "a region of tissue, or a molecule in a cell membrane, that responds specifically to a particular neurotransmitter, hormone, antigen, or other substance." Which I suppose is a fancy way of saying it's like an iPhone charger port. Your charger cord (Shiga toxin) only works for an iPhone port, and only a specific version of the iPhone port. Shiga toxins are able to bind (plug in) to Gb3 receptors. Kidneys have more Gb3 receptors than any other part of your body and kids' kidneys have more Gb3 receptors than adults. This is likely why kids are more likely to develop HUS due to an STEC infection than are adults. And also why HUS leads to kidney failure in up to 70% of patients. Some patients also have neurological symptoms like altered consciousness and seizures. The processes by which HUS causes kidney failure and other organ damage are complicated and I've already gone on for quite a long time spewing technical medical jargon so I'll spare you. Wikipedia has a pretty good page on HUS, as does Medscape, if you're so inclined. 

Treatment for HUS is largely supportive and may include dialysis while the kidneys recover. Treatment of the STEC infection with antibiotics is not generally recommended; there is some evidence to suggest that the bacteria release more toxins, leading to increased risk of HUS. Other evidence shows certain antibiotics may prevent HUS. More studies are needed. What we do know is that antibiotic treatment has little effect on the duration or severity of the gastrointestinal infection symptoms.

So what can you do? 
I talked about how STEC infections end up in the news when there is an outbreak of illness associated with contaminated food. I think most people of a certain age associate O157 with undercooked hamburger because of a large outbreak associated with eating hamburgers from a popular fast food restaurant called Jack In The Box. We know that undercooked meat can make us sick and we take steps to ensure that doesn't happen. What many people don't realize, however, is that cooking meat properly does nothing to stop contamination of the side salad from using the same cutting board or utensils for handling both raw meat and vegetables. 

People may also not be aware the same bacteria that can be found in hamburger meat can also be found in other foods like raw flour, lettuce and other leafy greens, sprouts, raw (unpasteurized) milk, and pretty much anything else that has come into contact with poop contaminated with STEC. STECs are found in the guts of ruminants like goats, sheep, deer, and cattle. These animals don't have any of the Gb3 receptors we talked about earlier, so they don't show symptoms. The bacteria are just living in the gut and hitch a ride out of the body on occasion in the animal's poop. You may have noticed cattle, goats, and others don't concern themselves with hygiene the way we humans do. They just poop and walk away. Sometimes the poop is a little loose and runs down a leg or splatters on an utter; sometimes they walk in it and spread it around on their hooves. Animals in fields, barns, large-scale feed lots, and petting zoos may take a snooze on a hot day and lay down in their own feces and the poo of their pals. The bacteria in the poop get transferred to the animal's hide. Then we head to the petting zoo and give that cute little animal a hug or a pet or a scratch. And if we're a little kid, we pretty much instantly put our hand in our mouth. Animals carrying STEC may graze near a field of lettuce, or that field of lettuce may be fertilized with cattle feces that hasn't been properly composted to reduce the numbers of bacteria. Insects, birds, and rodents can pick up STEC on their feet and transfer those bacteria to a field of wheat. 

I don't want to make it seem like there isn't anything you can do. There is! Following safe food handling guidelines and hand hygiene are the best ways to protect yourself and your family.
  • Never eat raw or undercooked ground beef and cook all meat thoroughly according to guidelines
  • Don't drink raw milk and FOR THE LOVE OF EVERYTHING DON'T GIVE IT TO YOUR CHILD
  • Dedicate one cutting board and utensils for handling meat and another for vegetables
  • Wash cutting boards, utensils, and counters after handling raw meat
  • Don't eat raw or undercooked dough
  • Wash your hands before cooking, after handling raw meat, and before you eat
  • Wash your hands and your children's hands when at a petting zoo or fair or carnival or any other place where you have encountered and touched animals and their surroundings
  • Wash your hands after handling dirty diapers and helping kids use the bathroom
  • Avoid swallowing water in lakes, streams, ponds, swimming pools, and splash pads
I hope I didn't freak you out too much. Be safe and have a happy summer!