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:

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.


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.




Why Isn’t Campylobacter Better Known? – By Hannah Bolinger

If you have read What is Campylobacter, you will know that it is a top five foodborne pathogen for illness, hospitalization, and death. With that being the case it is remarkable that Campylobacter is still an relatively unknown pathogen. However, there are a few reasons for this including the self-limiting and sporadic nature of the disease, and under reporting of illnesses.

Campylobacteriosis most often occurs as a sporadic illness i.e. a common source for an outbreak is not noted. This tends to draw less attention from both the media and government agencies than the large multi-state outbreaks that we sometimes hear about.  However, larger outbreaks of Campylobacter can occur and are often the result of unpasteurized milk or untreated water.

Campylobacteriosis is also known as being a relatively minor illness. This is true in the sense that most people will recover from their gastrointestinal discomfort without needing to see a doctor. However, illness can also be extremely acute with the pains sometimes mimicking appendicitis. Campylobacter also has the potential of causing more serious infections in the very young, old, pregnant, or immunocompromised. After a Campylobacter infection there is the potential for autoimmune complications such as Guillain-Barré syndrome, a form of reversible paralysis. Those suffering from Guillain-Barré may take months to recover and may require respiratory support. Another autoimmune complication that can follow a Campylobacter infection is reactive arthritis, characterized by painful joints, eye, and urinary tract problems.

Finally, under reporting is another contributor as to why this disease is not discussed more. Because most healthy adults will recover on their own, it is estimated that only about 1 in 31 cases is reported. Many patients do not seek medical care. Even if a patient does seek medical attention, it is not guaranteed that the doctor will perform a culture-based diagnosis. So, there may not be a definitive conclusion as to what caused the illness. Doctors may treat a patient based on one’s symptoms, and because the symptoms of Campylobacter are nearly indistinguishable from other agents that may cause gastroenteritis e.g., diarrhea and/or cramping, doctors may prescribe antibiotics that may not be optimal for treating campylobacteriosis.

It is likely that Campylobacter infections occur much more often than reported. Because the illness can be mild and of relatively short duration patients do not always seek medical care. However, even if they do it is not guaranteed that a specific etiologic agent will be identified. And, because large outbreaks are rare the media does not give this pathogen the same coverage as others which may cause more severe illness or larger outbreaks. But, because of the high number of illnesses, and the potential for severe infections and autoimmune sequelae Campylobacter should be treated as a much more important foodborne pathogen.

Campylobacter Biofilms: A Super Resistant Army


By Kshipra Chandrashekhar

C. jejuni doesn’t show up so much in the headlines due to the self-limiting nature of infection. In developed countries like the United States, incidences of campylobacteriosis are more of an economic burden than a medical liability. Campylobacter is commonly found in the gastrointestinal tract of birds, cattle and the agricultural environment, acting as reservoirs of infection. Although Campylobacter is a fastidious organism with stringent growth requirements such as decreased tolerance to atmospheric oxygen, their ability to survive and thrive in the environment gives rise to the ‘Campylobacter conundrum’ which the poultry industry is trying to tackle. There are several ways by which Campylobacter infection can be controlled. Firstly at the farm level, by preventing the colonization of Campylobacter in poultry through the implementation of strict biosecurity measures. Secondly, by decreasing the bacterial load during handing of chicken in the abattoir and the production facility. To plan effective intervention strategies for Campylobacter control, a better understanding of Campylobacter survival under nutrient poor conditions outside the poultry gastrointestinal tract is crucial.

Biofilm is a community of single or multiple species of bacteria, held together in a slimy complex sugar matrix attached to a surface. Bacterial biofilms are extremely resistant to antimicrobials and disinfectants thus offering a continuous source of infection. Recent studies have shown that C. jejuni were able to persist in poultry slaughterhouses and food manufacturing units. Campylobacter gets attached to surfaces such as the chicken skin and plastic surfaces acting as a source of persistent contamination, thus resisting routine cleaning procedures. The formation of biofilms by Campylobacter has been identified to play a role in its ability to withstand environmental stresses, such as heating, chilling and exposure to chemicals, commonly followed during carcass cleaning. Campylobacter jejuni can form biofilms on abiotic surfaces and is also capable of colonizing pre-existing biofilms. There is increasing evidence that biofilms play an imminent role in transmission of Campylobacter through the food chain. Studies indicate that Campylobacter can better survive atmospheric conditions in biofilms. Surfaces at the meat processing facility and at farms that are prone to biofilm formation include dressing, washing and packaging tables, facility floor, cutting utensils, plastic surfaces of the feeders and watering distribution systems; therefore acting as a source of Campylobacter contamination. Food processing facilities can have the perfect environment for Campylobacter biofilm formation because of organic material build up on surfaces. These organic layers are rich in nutrients containing carbohydrates, lipids and sugars, creating a good surface for bacterial attachment and survival. Studies have also shown that soiling of surfaces with chicken juice positively impacts Campylobacter biofilm formation.

Seen below is a Campylobacter biofilm formed on a plastic surface (Pic courtesy: Dr Louise Salt, IFR, UK)


Most bacterial biofilms in nature are made up of multiple species. Studies have shown that Campylobacter can form single species (Campylobacter only) as well as mixed species biofilm, which provide a good environment for their survival due to the reduced oxygen levels in such biofilms. Campylobacter is able to form mixed species biofilms with Pseudomonas, which is a chicken carcass spoilage bacteria. Mixed species biofilms also act as a source of nutrient exchange, aiding in Campylobacter survival in such an environment.

These findings from Campylobacter studies epitomize the challenges faced by the poultry industry and food producers. The resilience of Campylobacter biofilms gives them the ability to thrive under adverse conditions. A better understanding of the mechanisms involved in biofilm formation is essential in developing cleaning programs, subsequently decreasing the persistence and transmission of Campylobacter. Strategies to eliminate such reservoirs of Campylobacter during food manufacture will certainly bring a positive impact on our efforts to reduce the incidence and transmission of Campylobacteriosis and other food borne infections throughout the food chain.


IAFP Abstract Erythromycin Resistant C. jejuni Information

The Kathariou lab will be presenting some of our research at the annual IAFP meeting this year.  Below is the abstract and information on the poster that is being presented at the conference.  If you’re there come and check out our research into the spread of erythromycin resistance.

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