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).

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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.

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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.

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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.

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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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