new article by Kathariou lab on macrolide resistance in Campy!

We had a new article in Foodborne Pathogens and Disease.

Lack of Evidence for erm(B) Infiltration Into Erythromycin-Resistant Campylobacter coli and Campylobacter jejuni from Commercial Turkey Production in Eastern North Carolina: A Major Turkey-Growing Region in the United States.

Bolinger HK, Zhang Q, Miller WG, Kathariou S.

Foodborne Pathog Dis. 2018 Aug 10. doi: 10.1089/fpd.2018.2477. [Epub ahead of print]

PMID:
30096008

Cottage Foods: Combating Antibiotic Resistance Locally?

A lot of things have changed in 2016 (and even early 2017) but at least we all still have one thing in common: we all eat.  An increasing number of people put a premium on eating healthy food from local farmers.  In fact, numerous states consider local food an import part of their identity and economy.  With the thought of promoting agritourism, attracting tourists and visitors to a farm or ranch, and local businesses, many states have introduced cottage foods bills and laws.

But what’s a cottage food?  Is it made in a cottage?  Is it a form of cheese?  No-the definition is actually much broader than either of those.

Cottage foods are defined as non-potentially hazardous food products that are made in someone’s residence as part of a business. These products are allowed for sale in several different states under slightly different laws and regulations.  The largest issue with these products is that producing food in someone’s home can be a recipe for microbial hazards, like contamination with Salmonella or Listeria.

(Image from United States Library of Congress, LC-USW36-949)

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Antibiotic Resistance Trifecta: Interactions of Antibiotics, Microbes, and the Gut Microbiome

There are many concerns about how the gut microbiota is impacted by antibiotics.  Since the widespread use, and sometimes over use of antibiotics began around 80 years ago, bacterial antibiotics has increase worldwide.  This makes bacterial infections harder to treat and increases the risk of severe side effects.  If was only this year in January that a woman died from a bacterial infection contracted after surgery that was resistant to 23 different antibiotics.

It’s clear that bacterial antibiotic resistance has risen alarmingly.  What is less clear is how those antibiotics effect the gut microflora.  Studies recently performed have shown that a dysbiosis, an “unbalanced” or abnormal state of the microbiome, in the gut can cause unchecked microbial growth of low abundance organisms known as opportunistic pathogens.  These opportunists are usually kept in check by other dominant microbes but when those microbes decrease in number, the opportunists can grow unchecked and cause devastating health issues.

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Resources on Antibiotic Resistance and the Microbiome

Below are 2 excellent resource (curtsey of QIAGEN) that give a great background on antibiotic resistance in hospital infections and using metagenomic techniques to study the microbiome.  We do not claim ownership of the slides or any product, techniques, or studies used and are not attempting to promote them.  They all belong to QIAGEN and associated researchers.  We simply recognize the value of the introductory information and wish to share the slides for educational purposes.

The slide decks can be found online below:

Know Your Lingo 2.0: Landmark Microbiome and Metagenomic Projects

We’ve already gone over some of the basic terminology involved with microbiome studies (here) but some other key phrases frequently come up when discussing microbiome studies.  These phrases usually reference several landmark studies that deal with the microbiome.  Here we will review some of the most important landmark studies that will likely be discussed or encountered in microbiome research.

Human Microbiome Project– The full name of this project is “The NIH Human Microbiome Project” but in casual conversation the “NIH” portion is sometimes left off.  This was one of the first major efforts to study the human microbiome that utilized Next Generation high-throughput sequencing and involved many prominent microbiome researchers, such as Rob Knight.  The health implications of such a project are astounding and provide us with a much more comprehensive understanding of the microbes that live inside us.  If you happen to be in the Raleigh, NC area the Museum of Natural Sciences has a phenomenal and engaging exhibit that highlights research done for the NIH Human Microbiome Project.  It’s called “The Secret World Inside You”, go see it!

Sargasso Sea– The Sargasso Sea is a region of the North Atlantic Ocean and contains the island of Bermuda.  But why would this body of water be referenced by microbial ecologists?  Well, it was actually part of Global Ocean Sampling Survey (GOS) conducted by J. Craig Venter, think sequencing the human genome, and his colleagues.  They initially suspected low microbial diversity but after performing shotgun sequencing, they discovered a vast array of microbes present.  Perhaps the most surprising result was the huge amount of viral DNA present in the Sargasso Sea when compared to the other areas sampled.  The GOS radically shifted how we think of oceanic diversity.

Earth Microbiome Project– This ambitious project was started by Rob Knight and Jack Gilbert as a way to map the microbiomes of different environments all over the world.  Being able to transpose that information onto a global map would be insanely cool and relevant with global warming and environmental policy changing around the world all the time.  Mapping the microbiomes around the world is a huge undertaking and as a result requires massive global collaborations and that’s not even the hardest part.  With a plethora or researchers comes a plethora of techniques, which can be advantageous but can also result in incomparable results.  In order to combat this, the Earth Microbiome Project requires that a standard set of protocols be followed in order to submit your information to them.  Everyone uses the same kits, primers, and file types to ensure that the samples are processed in the same way.  Standardization of protocols and global collaboration make this project groundbreaking.

Wildlife of Our Homes– How do you get people involved and interested in science?  One way is to put them right in the thick of the experiment.  The Wildlife of our Homes does just that with its citizen science approach, which means the public and not just scientists are involved.  Headed up by Robb Dunn (NCSU- Go Wolfpack!), the project had people take swabs from designated areas around their homes and send them research labs for processing.  After providing relevant information about the number of family members, where they had pets, location, and other details, the results for different homes could be seen for different states, rooms, and much more.  By not only engaging the public but using the home as a model, Robb Dunn shows the public that microbes are everywhere and science is amazing.

American Gut– No you did not read that wrong.  The American Gut project is another citizen science project aimed to characterize, you guessed it, the American gut.  And army of researchers, including Rob Knight, Jeff Leach, Jack Gilbert, and Robb Dunn, collaborate on the support the project.  The American Gut project celebrates the diversity of Americans.  People from different ethnicities, locations, and backgrounds are encouraged to submit samples for analysis.  In a time when America can seem extremely divided, especially over science, implementing a project that celebrates our differences and emphasizes our commonalities is rare and greatly appreciated.  A British and Asia version of the project have also been slated.

Consortium For Sequencing The Food Supply Chain – This was created by IBM and MARS in 2015 to sequence to microbiome of the food supply chain.  They will be sequencing the core or “normal” microbiome of foods, processing plants, and even home counters.  The project looks at the bacterial, viral, and fungal DNA, which will provide a full picture of the microbial ecology of that food or surface.  Since this is a fairly new program there is still a lot of questions about how the project will work but with big names like BIO-RAD attaching themselves to it, it’s definitely one to watch.

If you want to learn more about any of these projects click on the project name and it will navigate you to their website.  Happy hunting and stay curious!

What Do Food Microbiology Students Know About Campylobacter?

We asked a class of university students taking Food Microbiology at North Carolina State University to fill out a survey regarding knowledge of Campylobacter. The class was composed of students from the Food Science department (denoted FS) and Microbiology department (MB). There were both undergraduate and graduate students in the course.

The first question asked the students if they had ever heard of Campylobacter. Of 57 students who participated in the survey, 34% responded “no” and 66% responded “yes”. The data was further divided and Fisher’s Exact tests were performed to see if the class (FS405, FS505, MB405 or MB505), major (Food Science or Microbiology) or rank (undergraduate or graduate) affected the outcome of having heard of this pathogen. There was no statistically significant effect of class on the outcome of whether or not students had heard of Campylobacter (p=0.298). Additionally, there was no effect from major ( food science or microbiology) or status (graduate vs. undergraduate) (p= .750 and .097 respectively).

campyplot

If participants answered yes to the first question, we then asked them if Campylobacter was a virus, a bacterium, or chemical. The vast majority (97%) of participants who had heard of Campylobacter knew that it is a bacterium.

what

Next, the participants were asked what percentage of foodborne illnesses caused by 31 known pathogens Campylobacter is responsible for? The most commonly reported answer was that Campylobacter is responsible for 25% of foodborne illnesses. The correct answer of 9% was selected by 30% of participants, and no participants selected chemical as a response.

illness

Next, the participants were asked where one might catch Campylobacter. The most common and a correct response (34%) is that Campylobacter is associated with poultry. However, 18% of respondents mistakenly thought that this might include eggs. Unpasteurized milk and dairy products was another common response (23%) and is also a correct answer. No respondents chose a sick friend as a mode of infection, and 18% of respondents chose produce.

Finally, participants were asked where they get information about foodborne outbreaks. The results were nearly equally split between social media (30%) and TV (29%). Word of mouth was also popular (15%). Print news (9%), radio (4%), government (5%), and other (8%) made up the rest. The “other” category commonly included other websites such as FoodSafetyNews.com which the students wrote in.

outbreak

It is not surprising that so many of the students taking Food Microbiology have heard of Campylobacter. These students take general microbiology, and might have learned about foodborne pathogens then. Students are over estimating the burden of reported foodborne diseases from Campylobacter in the U.S . They also do not have a clear understanding of the routes of transmission.

 This survey was administered at the beginning of the semester. It may help professors identify gaps in students’ knowledge regarding this organism. For example, students should understand that Norovirus and Salmonella are responsible for many more illnesses than Campylobacter. However, the possibility of serious consequences from campylobacteriosis makes this a serious organism to consider. Additionally, since Campylobacter is rarely responsible for large outbreaks, it may not make headlines. Survey participants get much of their news on social media and TV and may miss these reports.

2014 NARMS data released!

On November 18, 2016 the 2014 NARMS report was released. The report includes a brand new interactive tool that lets users choose which combination of pathogen, source, and antibiotic results they would like to see. It’s especially useful because it makes comparing current data to past results incredibly easy. The 2014 NARMS report tested a  total of 4,122 Campylobacter isolates from human clinical cases, turkeys, cattle, and swine.  33% of retail chickens carried Campylobacter, the lowest level since 2003. Additionally, 12% of chicken ceca was Campylobacter positive and 6.1% of turkey.

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Macrolide resistance is especially interesting to Campylobacter researchers because they are the first line therapies for human cases and are approved for use in all food-producing animals. Since testing began in 1997, macrolide resistance in C. jejuni has remained below 4%. In 2014, resistance to macrolides fell below 2% in all sources except market hogs. Macrolide resistance in C. coli is  much higher than in C. jejuni. In the 2012-2013 NARMS report the incidence had more than doubled in human, retail, and PR/HACCP chicken C. coli isolates. This led NARMS to consider whole genome sequencing (WGS) to test for the presence of the recently identified erm(B) gene. Noneof the 12 tested isolates carried erm(B). These resistant isolates carried previously identified mutations in the 23 S ribosomal gene, and were not genetically similar indicating that there has not been clonal expansion of this resistance in Campylobacter.

Fluoroquinolones (e.g. ciprofloxacin and nalidixic acid) were banned for use in poultry in 2005. NARMS data indicates that resistance to fluoroquinolones in C. jejuni isolated from humans has reached the highest level since NARMS testing began in 1998. This is important as the fluoroquinolones are an alternative treatment for campylobacteriosis. Retail chicken and PR/HACCP chicken isolates also experienced increased incidence of resistance. Fluoroquinolone resistance could not be determined because of the number of turkey-derived C. jejuni  isolates (n=1). Of the 15 C. coli isolates from turkeys, approximately 40% were resistant to fluoroquinolones.

1.4% of the 1,251 C. jejuni isolates from humans were resistant to gentamicin. None of the eight C. jejuni from chicken ceca or the 369 retail chicken isolates were resistant to gentamicin. To the best of the author’s knowledge, no C. jejuni from turkeys were tested for resistance to gentamicin. This may be due to there only being one C. jejuni isolated from turkeys. However, 13.3% of the 15 C. coli isolates taken from turkey ceca were found to be gentamicin resistant. The Kathariou lab utilizes the yearly NARMS reports for much of their research. Check out more of our website to see what the Kathariou lab is doing to monitor antibiotic resistance in Campylobacter.

 

 

 

Know Your Lingo: How to Read Microbiome and Metagenomic Articles

With the advent of metagenomic studies, scientists need to understand the terminology used in them.  Much like metagenomics itself, the vocabulary used contains words from multiple disciplines such as ecology, bioinformatics, and microbiology. However, these terms may have slightly different meaning and nuances when used in metagenomics studies.  To help clear up the usage of some of these terms and provide a little back ground on them, I have complied a guide that breaks down the meaning and associated nuances for some of the most frequently used terms in metagenomics studies.

Microbiome- All the microbial (bacterial, fungal, viral, eukaryote, or a combination of any of these) DNA in an environment, community, or ecosystem.  This data is usually obtained by use of high throughput sequencing.  This term functions as a microbial census of “who is there?”  Results can be obtained through 16S, 18S, and ITS markers (which will be defined more fully later.)  Because microbiomes are composed of DNA found through sequencing, just because an organisms’ DNA is part of the microbiome doesn’t mean that organism is alive within the community.

Microbiota- All the microbes (bacterial, fungal, viral, eukaryote, or a combination of any of these) in an environment, community, or ecosystem.  This is subtly different from the microbiome because it describes all of the organisms present, not just the DNA found.  These microbes are the ones alive and functioning in a particular environment, community, or ecosystem and can also encompass all microbes, bacteria, fungi, virus, or some eukaryotes.

Metagenomics- The genetic analysis of microorganisms in conjunction with relevant data.  These studies extract total DNA from a sample and collect information about that sample that can be useful in analysis.  These studies often revolve around “who is there” and/or “what are they doing”.  By characterizing a microbial community and learning how that microbial community functions, or shifts can provide insight into microbial based intervention and a greater understanding of microbial ecology.

WGS- This is an acronym that stands for “Whole Genome Shotgun Sequencing”, sometime this is just referred to as “Shotgun”.  WGS is method of determining the entire sequence of a genome (for example a bacterial genome) by the use of sequencing fragments of the genome and piecing them back together.  The genome is broken into small segments which are then sequenced and put back together with a reference genome or de novo (done without a reference) by utilizing to overlapping portions of the segment.  The FDA is employing this kind of methodology in GenomeTrackr to aid in outbreak tracking and identification.

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CALS Stewards of the Future: Collaboration and Microbiomes

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Microbiomes are the future.  Versions of this statement have been uttered time and again by some of the most influential minds in science.  The CALS Stewards of the future seminar at NCSU echoed this call in late October with an entire day focused on studying the microbiome, the implications these studies have on the future of science, and how collaboration is needed to succeed.  The talks ranged from basic to applied studies and emphasized how this technology could be applied to agricultural fields. Continue reading