E. coli in our lakes: what does it really mean?

If you follow the local news, or have children that love swimming, you have probably noticed an increasing number of beaches in Minnesota closed recently due to high E. coli levels. Just in Minneapolis, Lake Hiawatha Beach and Lake Calhoun’s Thomas and 32nd Street beaches were recently closed in response to high E. coli counts in the water. The simple phrase “E. coli” strikes fear into the hearts of anyone who has ever experienced gastrointestinal distress. However, it is important to understand what E. coli actually is and what “high E. coli levels” actually means to our lakes.

What is E. coliE. coli stands for Escherichia coli. This is the formal name for a species of bacteria in honor of the German-Austrian physician Theodor Escherich, who first identified the bacteria associated with digestion in infants. Here are the important take-home messages about E. coli:

1. We all carry about 1,000,000 E. coli cells per gram of feces in our guts. That’s right, over 1 million E. coli per gram of poop! If you are healthy, none of these E. coli are capable of causing gastrointestinal illness. In fact, gastrointestinal disease (i.e., diarrhea) due to E. coli is extremely rare in the U.S. and other industrialized countries. We tend to think of E. coli as bad because of the popular press, but in actuality these are important components of a healthy gut in animals (including us).

2. We are not the only animals that carry E. coli. Nearly every mammal and bird carries E. coli. And, there are many different “flavors” of E. coli. Some can colonize birds, some can colonize humans, some can colonize pigs, some can colonize cattle, and some can colonize all of these animals. So, one E. coli certainly does not equal all.

3. Fecal coliform and E. coli counts do not necessarily mean that pathogens capable of causing disease are in the water. It is very important to understand what “high E. coli levels” means when they are found in lakes. E. coli levels are established, according to the Minnesota Department of Health, through testing of water samples from Minnesota beaches. They take these samples and perform culturing of the samples to determine how many E. coli are present in 100 mL of water (100 mL is slightly more than 3 ounces of water). Over a 30-day period, the number of E. coli cells should not exceed 200 per 100 mL of water, on average. Also, no single sample should ever exceed 1,000 E. coli cells per 100 mL of water. If these criteria are exceeded, then closure of a beach is recommended until the numbers of E. coli go down. Remember, these are generic counts of E. coli cells in the water. The actual source of these E. coli are unknown. In fact, they likely originate from a multitude of possible sources, including human waste, bird droppings, agricultural run-off, or even naturally occurring E. coli present in the soil. In short, an E. coli count of 1,000 cells per 100 mL does not means that there are 1,000 E. coli cells that can make you sick per 100 mL of water. It is actually quite likely that none of these E. coli will make you sick. The reason that the department of health uses these criteria is based on the likelihood of pathogens (not just E. coli, but other pathogens as well) being present in the water based on the counts of E. coli as an “indicator organism.” This is a very conservative approach to estimate the possibility that pathogens are in the lake water.

4. What about the E. coli that can cause disease? So let’s assume that the lake we are going to swim at does harbor some pathogenic E. coli or other pathogen. We have to consider something called “infectious dose,” or how many cells of the pathogen it actually takes to make you ill. Remember I said before that at best, a small fraction of the E. coli present in lake water will actually be capable of causing disease in humans. The only way it can make you sick is through oral ingestion (the infamous fecal-oral route). And, for healthy humans, the infectious dose of E. coli (only the ones able to cause disease) needs to be in the range of 100-10000 cells. Obviously, you can ingest these bacteria even if you don’t drink the lake water. However, typically in order to acquire enough of the pathogenic bacteria you would have to swallow water, in my opinion. If you have young kids, you know all about swallowing water. Yes, it happens.

So why should I be worried? There really shouldn’t be any cause for alarm when these alerts go out. The department of health is looking out for your best interests, with good reason, to prevent the occurrence of disease acquired through swimming. I am not recommending that you do not heed their warnings! These warnings are established, like I said, through a conservative approach to ensure that you don’t get sick when you swim. In my opinion, most of these alerts are likely benign, and only a small percentage of “high E. coli level” lakes actually contain pathogens capable of causing human disease. However, I am not willing to play the pathogen lottery with my kids or my family, and I wouldn’t recommend that anyone do that. Until we have better and cheaper ways to measure pathogens in lake water, this is the best we have and it is in place for a reason. But there is no reason to panic. Like I said before, these E. coli can arise for a lot of different reasons, they don’t always correlate with microbes that can make you sick, and they will go down over time. So, my advice? Pick a different lake this week, and don’t hesitate to return to your favorite lake when the alert subsides! Oh, and don’t blame the E. coli.

iComos 2014: conference re-cap and tweets

The first International Conference on One Medicine, One Science (iComos) was held at the University of Minnesota from April 27-29, 2014. The conference just wrapped up, so I wanted to re-cap on what I think was an excellent conference.

The goal of the conference was to “explore the science of animal health in complex environments from molecular/cellular interactions to ecosystem/landscape levels.” Unlike most science conferences that I have attended where there is a specific disciplinary focus (i.e., microbiology, genomics, avian disease, etc.), this conference brought together a huge range of disciplines centering around the science behind the concept of one health. A few notable speakers included Nobel Laureate Peter Agre talking about aquaporins, Samuel Thevasagayam from the Gates Foundation speaking about Gates’ vision of One Health, James Lloyd-Smith from UCLA talking about smallpox/monkeypox, Sonny Ramaswamy from USDA-NIFA talking about food animal domestication, Mehmood Khan of PepsiCo talking about beverage challenges and opportunities, Jonathan Foley from UMN talking about global food production, Marla Spivak from UMN talking about the bee crisis, Andrew Zimmern from the Travel Channel talking about food across the world, and Stanley Maloy from SDSU talking about the evolution of pathogens. So, from the list you can see that it spanned a range of disciplines and brought together a lot of people that would not normally congregate.

Did the conference accomplish its goals? I would say it did for an inaugural conference. The key emphasis of the conference really moved towards defining and addressing one health from many different perspectives. Different opinions were presented and challenged, which is a very good thing in a collegial atmosphere. Moving forward, I think it became evident that science-based decision making needs to be a priority related to one health. Multiple times, it was stressed that public perception often overrides science-based decision making in our government. One of the best points presented throughout the conference is that we (as scientists) need to do a better job of outreach through social media. With that said, I was delighted to see an active twitter feed throughout the conference (pasted below). So, there is hope for us as scientists to continue to become more active in this arena. This needs to be better supported by the institutions that employ us as a part of our job, because it is exactly that.

Overall, iComos was a success and I look forward to many more in the future!


Tweets from #iComosUMN


The story behind “Light Turkey Syndrome” in Minnesota

Our lab recently published an article in PeerJ describing the succession of the bacterial microbiome in the ileum of commercial turkeys, and the relationship between this bacterial succession and a condition known as Light Turkey Syndrome or LTS. I thought it might be useful to describe the history surrounding this condition in a little more detail.

LTS has been talked about by commercial turkey growers in Minnesota for nearly 10 years. When I first started talking to industry people about LTS, several notable observations surfaced. First, this condition is different than classical disease conditions with known pathology in commercial turkeys. LTS does not involve any known pathology in the digestive or respiratory systems. This is different from a condition known as Poult Enteritis and Mortality Syndrome (PEMS), where there is notable watery droppings in poults, dehydration, stunting, spiked mortality, and acute enteritis. LTS is a benign condition, with only two primary observations that are considered abnormal: 1) high variations in weights between poults within a flock, and 2) lower-than-average flock market weights on the order of 1-3 pounds per bird. 

So, LTS is a problem that is much different than classical diseases seen in the turkey industry over the past fifty years. Dr. Sally Noll’s lab first looked at flocks experiencing LTS to see if there were any notable differences between lighter and heavier birds within the same commercial flock. They first looked for some common gut pathogens, including Salmonella, Campylobacter, E. coli, astroviruses, rotaviruses, and reoviruses. They found no differences between lighter and heavier birds in the presence of these potential pathogens, and they found no differences overall between lighter and heavier flocks for the presence of these potential pathogens. They also did histological analyses of gut and immune tissue and measured xylose absorption on these birds, and found no major differences between light and heavy birds/flocks. To some extent, this ruled out active disease, gut development, and immune status as causes of LTS.

What about external factors? Here are some anecdotal observations. Poults hatched from the same source in Minnesota go to farms within Minnesota and elsewhere in the world. The industry has tracked the market weights of these flocks over a number of years, on farms that have very similar management systems and similar nutritional plans. Based upon an expected market weight established using flocks outside of Minnesota, the vast majority of flocks within Minnesota rarely achieve these weights. 

LTS can be reproduced via inoculation studies. Inoculation of research flocks with fecal homogenates from LTS flocks depresses growth. This suggests something about the gut microbiome that induces LTS. There are a lot of additional refined animal experiments that are needed to fully understand the nature of the gut microbiome-LTS relationship. Is there an unknown bacteria or virus in LTS flocks that asymptomatically depresses growth and performance? Or more likely, is it shifts in the entire gut microbiome that impacts growth and development? Now that we know the succession of bacteria in the turkey ileum and how it is impacted or slowed in LTS flocks, can we modulate it? And is this approach enough to solve the LTS problem?

What is a Superbug??


You hear it every day in the popular press. It instills fear upon its very mention in a news release. But what exactly is a “Superbug?”

Let’s start with a search for “Superbug” on the internet. I did a google search and came up with a few definitions:

Maryn McKenna is a science writer and author of the popular book “Superbug.” She has written some fantastic blogs under the Wired Science blog Superbug. Her book focused on methicillin-resistant Staphylococcus aureus (MRSA), and her blogs have had a major emphasis on multidrug resistant (MDR) bacteria and the implications of antibiotic use on the rise of MDR bacteria. So, it would seem from Maryn’s standpoint that MDR bacteria with pathogenic potential represent a Superbug. That seems pretty logical to me.

Wikipedia states that “pathogens resistant to multiple antibiotics are considered multidrug resistant (MDR) or, more colloquially, superbugs.” States the same that McKenna implies.

Merriam-Webster dictionary defines Superbug as “a pathogenic microorganism and especially a bacterium that has developed resistance to the medications normally used against it.”

It looks like most sources agree on the definition of a Superbug. A pretty simple and straightforward one at that.

Now we get into shades of grey. What if we have trouble defining MDR and/or defining pathogen? For example, what if we find an MDR E. coli isolate on retail chicken such as that reported in the recent Consumer Reports investigation? The authors of this article spend a great deal of time discussing the implications of pathogen contamination of retail meat. But, if you look at the data, the prevalence of true pathogens of concern (such as Salmonella) is actually quite low, while E. coli isolation is more frequent. Still, they lump these together as “presence of bacteria on retail meat”. To make it clear, the classical diarrheagenic E. coli such as O157:H7 are not found on chicken. The biggest risk of E. coli in chicken is that some of these E. coli may have the potential to cause extraintestinal infections in humans, such as urinary tract infections (although this is still a controversial topic). However, the majority of E. coli from poultry do not seem to possess this potential. Survey studies such as the one conducted by Consumer Reports do not distinguish between whether or not an E. coli isolated from a chicken breast actually represents a possible human pathogen.

Let’s also look at the same report and their discussion of MDR. Their data (presented here) illustrates that MDR in pathogens of concern is again very low. Yet, they chose to lump all bacteria together in statements such as “Our test results found that 49.7 percent of our samples contained at least one multidrug-resistant bacterium.” This is again a shady area of the use of the word Superbug, since by definition it is a pathogen that has acquired MDR. Lumping all of these bacteria together as potential Superbugs is not appropriate. If the data were parsed to categorize Superbugs by pathogen type and MDR phenotype, then the data would be much less convincing. While it is convenient and sensational to lump them all together, it is an inappropriate use of the data.

Fortunately, the CDC is taking a lead on a better definition of Superbug. An article in CNN describes CDC’s proposal to categorize Superbugs by threat level. The levels are “urgent,” “serious,” and “concerning.” Those falling in the urgent category include MDR Clostridium difficile (C dif infections), carbapenem resistant Enterobacteriaceae (Klebsiella, E. coli, and Salmonella resistant to carbapenems), and Neisseria gonorrhoeae (causative agent of gonorrhoeae).

So, it seems that we are on the path to appropriately defining a Superbug, taking into account not only that a pathogen is MDR but also the ability of said pathogen to cause disease and hamper antibiotic treatment. A final issue is what policies should be taken to reduce the spread of these Superbugs. Here is probably the most important point – not all Superbugs become so in the same way. Some, such as CRE, pick up plasmids that make them MDR. Others acquire mutations that make them MDR over time. And they all spread differently, some through horizontal gene transfer, some through clonal dissemination, some using both. It is frustrating to see the media and activist groups misuse definitions to promote an agenda. Take, for example, the National Resources Defense Council, which starts this recent article with the following statement: “Feeding low levels of antibiotics to cows, pigs and chickens that aren’t even sick breeds “super bugs” — dangerous germs that are able to fight off antibiotics that spread to our communities and families.”

Now, I don’t disagree that we should judiciously use antibiotics in all settings, including animals. But as I have stated before, blanket statements such as the above one by NRDC are inappropriate. First, it implies that Superbugs as a whole are all impacted by use of subtherapeutic antibiotics in animal agriculture. Not true. Also, none of these reports ever reference articles demonstrating that subtherapeutic use of antibiotics in animals drives the emergence of Superbugs. I challenge you to do literature searches for articles demonstrating in a controlled experiment that this is the case. Believe me, I have tried, and there is nothing out there that convincingly demonstrates that this happens. This is why USDA/FDA have been lobbying for educated removal of certain drugs from animal production versus the mass removal of all antibiotics under a given claim. I think we really need to better consider the underlying science of policy making in this country, and support more science to make better decisions.

All this said, Superbugs are real. The name provokes a lot of unimaginable thoughts to people reading an article. We as humans are very good at sensationalizing and placing blame, less effective at promoting the right forms of change. Using a more concise definition of Superbug, let’s also promote the necessary science to address issues and solutions, rather than using public fear to promote changes in the absence of science.

The turkey microbiome – a fitting Thanksgiving tribute

Since turkeys are on the mind this time of year, I thought it would be fitting to write a little more about our work on the turkey bacterial microbiome. The link describing this project is here, and the direct link to a manuscript in revision at PeerJ is here. The project data is available here through MG-RAST. The entire point of this project from the beginning was to 1) identify the bacteria in the gastrointestinal tract of the commercial turkeys over time, 2) identify differences in the microbiomes of high-performing versus poor-performing birds, and 3) develop diagnostic tools to predict performance outcome in a bird based upon ileum microbiome. The long-term goal of this project is to identify antibiotic-free alternatives to modulate the gut and improve turkey health and performance.

I’m writing this post, in part, because we are nearly finished with the descriptive portion of the project and moving on to the animal experiments aimed at modulating the turkey microbiome. First, what have we learned? Much of what we have learned is not so surprising, but some of what we have learned is quite interesting. We looked at the bacterial populations in the turkey ileum via 16S rRNA profiling using MiSeq on the V3 hypervariable region. First, the not-so-surprising. The ileum microbiome diversifies with age. It also stabilizes with age. And age is more of a driver of the ileum microbiome than are environment or treatment effects.

Now, the interesting. There were a number of specific markers (note I say markers and not drivers) of gut development in the bacterial microbiome, including several notable Lactobacillus species (L. aviarius, L. johnsonii, etc.). More prominent of a marker was a segmented filamentous bacteria (SFB) known as Candidatus division Arthromitus. These SFB bacteria were positively associated with high-performing flocks. What was interesting was that SFBs were of very short duration in the ileum, less than two weeks on average. After SFBs appeared, and disappeared, along came the other notable Lactobacillus species. This same pattern was observed in all birds in multiple flocks studied. However, the timing of this succession differed from bird-to-bird and flock-to-flock. The pattern that stood out was that the shift in microbiome occurred earlier in flocks performing better than their counterparts, suggesting a correlation between bacterial community succession and flock performance.

Now we are faced with a lot of lingering questions. There might be a cause-effect relationship between the ileum microbiome and immune system development, nutrient utilization, and ultimately growth of the bird. If there is a causative effect of modulating the microbiome, then it should be relatively straightforward to test such a hypothesis through animal inoculation experiments with cultured bacteria. But, animal experiments are costly and time consuming. We don’t know the best timing of inoculations, best combinations of bacteria, best dosage of bacteria, etc. Not to mention that we need to culture these bacteria and find representative isolates to use for the challenges. And some bacteria such as SFBs are non-culturable and will require other approaches to collect and inoculate them. We are currently looking for some in vitro screens that can be used to better refine the list of microbes to study in the animal. This too can be challenging, as there are limited cell lines and immunological tools available for turkeys. This is an exciting project with huge potential, but a great deal of challenges lie ahead….

Comments and suggestions welcomed!!

Thanks hypothesis-generator, now back to the bench (or, why I love microbiome projects).

The collective turkey ileum microbiomeYes, I have fully jumped on the microbiome and metagenomics bandwagon.

In fact, I know of very few labs in my field that have not in some way latched on to studies involving the 16S rRNA surveys in the past few years. We watched as the pioneers developed some fantastic protocols for applying this method to next-gen sequencing. Then, as the Human Microbiome Project emerged and revealed a plethora of associations between the microbiome and health/disease. Next, as even bigger projects were unveiled, such as the Earth Microbiome Project, and sought to sequence the world’s microbes. All of which have been very fruitful and extremely cool.

Sure, there have been modest efforts to characterize the bacterial microbiomes of agricultural animals, but funding for animal ag (mostly through USDA or industry support) has always been a small fraction of what is available through NIH. However, just like with genome sequencing, 16S rRNA surveys are now very much in the hands of the people instead of the large centers and research groups. So, here we are now with the ability to perform these surveys for an extremely low cost.

This brings me to the point of this post. A few years back we got into the 16S rRNA surveying using 454 technology, then it quickly translated into the same using Illumina MiSeq. Sure, we went in with hypotheses (yes, they are necessary even for pilot projects and small industry dollars) – but the hypotheses were more of the “duh, yeah” questions. We hypothesized that differences would be observed between commercial turkeys of differing weights and flocks of different average daily weights. And, we hypothesized that a predictable succession of bacteria would occur in the turkey small intestine. But, we really did not know what those specific changes would be and why they might be important.

So, we collected samples and sequenced. And sequenced. And sequenced some more. We learned how to analyze these data. We looked at the obvious things. And then we looked at the not-so-obvious things. It was a fantastic fishing (or maybe hunting is more appropriate here) expedition. And it totally paid off. We found some really interesting differences in the species of Lactobacilli and Clostridium that change over time in the turkey gut. We found that the successional shifts in the bacteria in the ileum are predictable, and they occur earlier in research flocks where the birds perform better. The work is nearly published in PeerJ. Overall, it was a great success.

As we all have learned, correlation does not equal causation. We have a lot of correlative data to suggest how the turkey microbiome can be manipulated to improve health and performance. Now, we head back to the benchtop to validate these findings and go after the handful of interesting hypotheses that came from this work. I feel like this is the trend of science lately. Technology drives new hypotheses, then the classical approaches are necessary to figure things out (Look to Jeff Gordon’s recent paper for inspiration). There are scientists on both fringes of this, though. Some refuse to use the technology and actually lambast anyone who uses it as pseudoscientists without hypothesis-driven research programs. Then, there are those who do nothing but use the technology and probably deserve to be lambasted. Me? I don’t really care what anyone says. 16S rRNA microbiome surveys have generated or refined more questions for us than I could have dreamed up during the same time. I suspect that most of us fall somewhere in this zone, where we are using the approaches to generate interesting questions from correlative observations, then to go out and get funding to address those questions. 16S rRNA surveys (and probably soon to be better metagenomic approaches) have changed the way that I operate for the better, and I can’t wait for the data from our next survey study.

Salmonella and misinformation?

Every now and then we hear news of potential outbreaks of Salmonella linked to food products. If you have followed the news you will note a recent outbreak linked to raw chicken (an excellent article by Maryn McKenna is here). Many people, including myself, read these articles and then read comments posted below the articles. Comments are great because it connects the public with the author and allows for free discussion. However, I was amazed at the misinformation that is also spread via these forums. I thought it would be worthwhile to revisit Salmonella basics related to 1) cooking and 2) antimicrobial resistance.

1) Cooking. Salmonella are basically E. coli that have evolved to acquire the ability to become intracellular pathogens and cause both diarrhea and systemic disease. However, the basic cellular components between these bacteria are still the same. They are both Gram-negative bacterial cells that do not form spores. Salmonella also do not release toxins like Clostridium botulinum (the cause of botulism) that can kill you even when the bacteria are dead. Therefore, from a foodborne illness standpoint, heat is an extremely effective way to eliminate Salmonella. Cooking meat to an internal temperature of 165 degrees F will ensure that you have zero risk of getting a Salmonella infection from the food itself.

The mistake most people make, though, is in food preparation. The bacteria can be present on raw meat (you should always assume it is). Therefore, separating the “raw” food prep area from the cooked prep area, and washing everything including your hands immediately after dealing with raw product, will substantially reduce your chances of spreading live bacteria to somewhere where they can be ingested. Keep in mind that household pets can also be carriers of Salmonella! If you give your dog raw meat, he/she can then pass the live cells on to the kids that the dog licks five minutes later. Following these basic practices reduces your chances of getting Salmonella from meat at home to very little / none.

It’s also worth noting that regulations are in place to keep Salmonella counts on retail raw meats down. A division of USDA called FSIS monitors the amount of Salmonella-positive samples from live birds and raw meat coming from large commercial broiler and turkey operations. One might ask, “why allow any Salmonella in raw meat products?” A simple answer is that it is currently impossible to eliminate Salmonella from live poultry operations. Birds are an ideal niche for Salmonella because they can carry many of the human-relevant serovars of Salmonella asymptomatically, meaning birds carry the Salmonella in their guts and display no signs of illness. One might also reason that buying organic chicken and turkey is safer than conventionally-raised birds. In fact, there is no difference between these two types of meat, both contain Salmonella along with Campylobacter (example study here). From the time that humans have started raising chickens and turkeys, there has been Salmonella – and that is not going to change anytime soon.

The bigger danger is eating raw vegetable and other foods contaminated with Salmonella. The extensive list of Salmonella outbreaks on the CDC website include foods such as mangoes, cantaloupe, sprouts, nuts, and tomatoes. These present a much greater risk because you may not be cooking these food products. It is advisable to thoroughly wash any raw vegetables and even soak them if possible to reduce your chances of getting infected. Fortunately the presence of Salmonella on these types of food is much less common than on raw meats.

2) Antimicrobial resistance. A final point is that there is major concern about antimicrobial resistance in Salmonella. This is a valid and true concern, as it is evident that Salmonella along with many other pathogens are evolving to become resistant to many therapeutic options available for disease treatment. Fortunately, if you get a Salmonella infection it is very unlikely that you will require antibiotic treatment unless you are infant/elderly. This doesn’t discount though that many Salmonella are now resistant to the most commonly used drugs to treat these infections, and it presents a great risk to immunocompromised populations. Before we jump to conclusions about banning antibiotics from agriculture, though, we probably need to look in the mirror. I have no doubts that all antibiotic use in some way contributes to the emergence of antimicrobial resistant bacteria. However, there are many necessary scientific studies needed to get at the actual risk posed by different applications of antibiotics. For example, which is worse: treating with a very low concentration of an antibiotic not used in human disease therapy for extended time, or hitting with a high dose of an essential human antibiotic for short duration? There is a wealth of literature out there, but even among scientists there still exists debate about this topic. Before jumping to any legislative conclusions, we need more science and data to support these decisions.