Co-occurrence, co-localization, co-selection: Antimicrobial resistance in agriculture

Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear.



Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions.

We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa.

Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.

Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance genes if they are genetically linked. No links to bacterial membership were observed for these clusters of resistance genes. These findings urge deeper understanding of colocalization of resistance genes and mobile genetic elements in resistance islands and their distribution throughout antibiotic-exposed microbiomes. As governments seek to combat the rise in antibiotic resistance, a balance is sought between ensuring proper animal health and welfare and preserving medically important antibiotics for therapeutic use. Metagenomic and genomic monitoring will be critical to determine if resistance genes can be reduced in animal microbiomes, or if these gene clusters will continue to be coselected by antibiotics not deemed medically important for human health but used for growth promotion or by medically important antibiotics used therapeutically.

Clusters of antibiotic resistance genes enrich together stay together in swine agriculture

Timothy A. Johnsona,b,f, Robert D. Stedtfelda,c, Qiong Wanga, James R. Colea, Syed A. Hashshama,c, Torey Looftf, Yong-Guan Zhud,e, James M. Tiedjea,b


mBio, Volume 7, Number 2, doi: 10.1128/mBio.02214-15

A review on antimicrobial resistance in agriculture is also available.

In this article, the current knowledge and knowledge gaps in the emergence and spread of antimicrobial resistance (AMR) in livestock and plants and importance in terms of animal and human health are discussed. Some recommendations are provided for generation of the data required in order to develop risk assessments for AMR within agriculture and for risks through the food chain to animals and humans.

Sophie Thannera, David Drissnerb,  Fiona Walshc


mBio, Volume 7, Number 2, doi: 10.1128/mBio.02227-1

Imagine if this applied to food reviews: UK hotel guests outraged by fine for leaving bad review

A British budget hotel that fined a couple 100 pounds (AUD$180) for writing a bad review about it online has agreed to pay them back and drop its policy of penalising guests who do that, officials said.

bad.reviewTony and Jan Jenkinson told the BBC they discovered the charge on their credit card shortly after they called the hotel as a “filthy, dirty, rotten, stinking hovel” on the travel website TripAdvisor.

The Jenkinsons said that when they questioned the charge from the Broadway Hotel in Blackpool, a seaside town in north-western England, it pointed out the “no-bad-review policy” in its terms and conditions.

Blackpool Council, which investigated the case, said the hotel has now complied with its request to remove the policy.

Risk factors for microbial contamination in fruits and vegetables at the preharvest Level: A systematic review

An abstract from the current issue of Journal of Food Protection:

The objective of this study was to perform a systematic review of risk factors for contamination of fruits and vegetables with Listeria monocytogenes, Salmonella, and Escherichia coli O157:H7 at the preharvest level. Relevant studies were identified by searching six electronic databases: MEDLINE, EMBASE, CAB Abstracts, AGRIS, AGRICOLA, and FSTA, using the following thesaurus terms: L. monocytogenes, Salmonella, E. coli O157 AND fruit, vegetable. All search terms were exploded to find all related subheadings. To be eligible, studies had to be prospective controlled trials or observational studies at the preharvest level and had to show clear and sufficient information on the process in which the produce was contaminated. Of the 3,463 citations identified, 68 studies fulfilled the eligibility criteria. Most of these studies were on leafy greens and tomatoes. Six studies assessed produce contamination with respect to animal host-related risk factors, and 20 studies assessed contamination with respect to pathogen characteristics. Sixty-two studies assessed the association between produce contamination and factors related to produce, water, and soil, as well as local ecological conditions of the production location. While evaluations of many risk factors for preharvest-level produce contamination have been reported, the quality assessment of the reviewed studies confirmed the existence of solid evidence for only some of them, including growing produce on clay-type soil, the application of contaminated or non-pH-stabilized manure, and the use of spray irrigation with contaminated water, with a particular risk of contamination on the lower leaf surface. In conclusion, synthesis of the reviewed studies suggests that reducing microbial contamination of irrigation water and soil are the most effective targets for the prevention and control of produce contamination. Furthermore, this review provides an inventory of the evaluated risk factors, including those requiring more research.

Journal of Food Protection®, Volume 75, Number 11, November 2012 , pp. 2055-2081(27)

Park, Sangshin; Szonyi, Barbara; Gautam, Raju; Nightingale, Kendra; Anciso, Juan; Ivanek, Renata

California restaurants decry ‘Yelp extortion’

Continuing with the gangster theme, mobster hacks are using the Internet to collect points.

The Sacramento Bee reported a few days ago that restaurant owner Sonny Mayugba was given an offer he almost could not refuse two weeks ago.

Not by a local gangster, but by a user of a popular online review site,

Mayugba said the user threatened to blast the Red Rabbit Kitchen and Bar at 2718 J St., which Mayugba co-owns, on Yelp because he believed he and his party got food poisoning from their meals.

Mayugba said it was impossible to prove whether the man got food poisoning from the restaurant but offered to give him a $60 gift card to a restaurant of his choice. The man said he deserved $100. If the restaurant did not pay up, he said he would write a bad Yelp review and report him to health authorities.

Is what happened to the Red Rabbit Kitchen an isolated case? Or has the growth in popularity of restaurant review websites – which allow anyone to write and rate restaurants from one to five stars – created a new way for some people to get preferential treatment.

Restaurant owners say online websites have changed consumer behavior as many people rely more on citizen reviews than on reviews of professional critics or advertisements. Yelp had a monthly average of more than 71 million unique visitors and 27 million reviews worldwide this year from January to the end of March, the company said.

In the end, Mayugba said, he refused to give the man anything and is not sure if the man posted a review on Yelp. But he said the experience made him rethink the value of Yelp and websites like it, which he said he loves.

"I was so upset," Mayugba said. "He was taking something that was inherently good to use it as a tool to extort a restaurant. It was just so wrong."

Kristen Whisenand, public relations manager for Yelp, said in an email that the website allows for users and business owners to flag reviews that violate the website’s terms of service. If it is determined the review is fake, biased or malicious, it will be taken down.

"More people trust citizen reviews these days," said Mayugba, who started a social networking website for the restaurant industry in 2007.

"Social media is a wonderful thing for the world, but when its integrity is compromised, what is it worth?

Slander applies to Internet: legal warning over food-poison allegations in UK

A warning for armchair epidemiologists: people who make unsubstantiated allegations about food poisoning in reviews on user-generated websites such as TripAdvisor could face legal action.

“It’s almost impossible to say with any certainty that food poisoning came from any one meal, so making these kind of threats could potentially be libellous,” said Mark Harrington, chief executive of Check Safety First, a company specialising in food hygiene checks.

Mr Harrington told The Telegraph that fake restaurant reviews are being used to blackmail hoteliers. “There have been many reports that customers have blackmailed hoteliers by threatening to post false food-poisoning claims on TripAdvisor. It is scandalous.”

The news follows the Advertising Standards Authority’s (ASA) ruling that TripAdvisor can no longer claim or imply that all its reviews can be trusted.

Kwikchex, a reputation management company that brought the case to the ASA on behalf of hoteliers and restaurateurs, said there were thousands of such allegations of food poisoning in Britain and U.S.

“Almost none are reported to the proper authorities, let alone substantiated,” said a spokesman. “Sometimes the reviewer believes it is the truth, but has not reported it and has no understanding of gastro-intestinal infections.

“They usually just pick on the last place where they ate, when in fact the incubation period for such infections is usually one to two days and sometimes as long as a week.”

The spokesman added that this type of allegation can be used by competitors and disgruntled ex-employees to harm the business.

Can you cope? On-line reviews

Last May, it was reported that 195 of the 580 people served Easter Brunch at Luciano’s Cotton Club in Worcester, Mass. were struck by norovirus contracted from a sick employee, and the incident was chronicled on Yelp and a food safety site called

“I would really drive home the point that they had a problem, investigated to determine what it is, and outlined a plan for what we’re going to do from now on,” said Gregory Charland, founder and chief executive officer of Charland Technology, a Hubbardston-based company offering a wide range of technology services. “Organizations should use problems like that to really do some soul searching and figure out how and why this happened. The overriding concept to underline is that they are never going to have their name in the news about this again.”

(Hint, and it’s in the blog post: don’t let sick employees work, even at an Easter buffet).

Alex Barbosa, the restaurant’s manager, declined comment.

That’s one anecdote in a story about on-line reviewing, which some love and some hate.

Alec Lopez dislikes consumer-driven review websites like Yelp, TripAdvisor and UrbanSpoon.

The owner of Armsby Abey in Worcester, Mass. said, “I don’t read reviews often,” Mr. Lopez said. “I hate Yelp because it’s an unanswered forum for people to bitch. I feel like it’s a green light to voice your opinion without consequences.”

Worcester native Andrew Chandler, a 29-year-old medical student at the University of Massachusetts Medical School, had an unpleasant dining experience at Armsby Abbey, and chronicled it on Yelp.

“I was really sad to have done it, but I think that when a place isn’t responsive or accommodating, people should know about it. I was hoping Armsby Abbey would read it and respond. I think it goes a long way if a manager explains what the circumstances were, and how they’ll prevent the problem from happening again. Today, online reviews can make or break a customer’s decision.”

In September, Harvard Business School professor Michael Luca released research that found a one-star rating increase on Yelp directly led to a 5 percent to 9 percent boost in revenue for independent restaurants, with comparable projections for independents in other industries. Despite the growing influence of Yelp and similar websites, business owners like Mr. Lopez continue to ignore — or worse, incorrectly address — negative feedback when it comes in the form of an online review.

With 61 million monthly visitors and 22 million reviews online by the end of the third quarter last year, Yelp is the most popular online review destination for everything from dentists to dieticians. Yelp’s popularity is proof that consumers trust reviews written by the average Joe, and enjoy contributing their own 2 cents.

Wilson Wang, chef and owner of Baba Sushi in Worcester, said he checks online reviews of his restaurant “all the time,” monitoring what diners like — and don’t like.

Mr. Wang, whose customers’ reviews currently rank Baba Sushi 4.5 out of 5 stars on, said he doesn’t respond personally to people’s comments but rather sees such reviews “as a mirror” to reveal what could be done better. “We are on the high level and we are really proud,” he said last week.

Yelp and websites like it open the door for independent businesses with limited marketing budgets, giving them an opportunity to advertise through old-fashioned word of mouth in a high-tech world. They offer a safety net to consumers who, with a few keystrokes, can be reassured that trying something new — rather than falling back on the reliability of a chain — won’t be a waste of their money.

“Every time I’ve given a negative review and gotten some sort of constructive, non-judgmental response, I’ve made it a point to go back to whatever business it was and give them a clean slate,” said Amy Jamieson, a 42-year-old Yelp user and homemaker from Worcester. “If they’re willing to try again, so am I.”

Food, Inc. misses the mark: Food is a business

Two weeks ago I went to see Food, Inc. with a couple of food safety colleagues. Reference to the documentary pops up daily on blogs and listservs — most remark on how it will change buying patterns, it’s the modern-day version of The Jungle, and is a wake-up call to consumers about food.

I just don’t see it.

What I got out of the Food, Inc. experience (beyond some pretty decent popcorn) is that the food system is complex and that there are multiple influences — including business.

The documentary jumped around from issue to issue: chicken production is inhumane; food is controlled by corporations, corporations want to hide what they do from you; cheap food is bad for you; cheap food is unsafe; food could be produced more sustainably; corn is bad; corn is controlled by corporations; Monsanto is evil, etc.

It all spun out of control, concepts were oversimplified (like pathogenic E. coli appeared out of nowhere because of corn-fed beef and buying organic food is the way to go — but it also all comes from the big, controlling corporations, so maybe don’t buy it) and it left me empty at the end.

I guess I’m getting tired of the polarized representation of food issues, without the discussion of trade-offs or presentation of data.

The food safety story that was woven throughout the movie was of Kevin Kowalcyk, a 2-year-old boy who tragically died from an E. coli O157 infection linked to recalled ground beef. The horrible story needs to be told but the connection that was made to the other vignettes was tenuous. Kevin’s story deserves a movie all its own.

There were winners (Walmart looked great to me, especially around their frank discussion of organic foods) and losers (big chicken producers Tyson and Perdue who reportedly didn’t participate in the documentary). Being part of the documentary was a great opportunity for the big players to open up their doors and tell their stories.

Flashing text at the end of the movie spelled out the main message for those who weren’t following along: food buyers have choices. This definitely fits in with a lot of what we’ve written about, and isn’t new — encourage individuals to ask questions about where their food comes from (what conditions it is grown under , what the producer/retailer/cook/server knows about food safety). Demanding labels (as was mentioned) isn’t nearly enough — we should be provided with data and a chance to make an informed choice.

Unpasteurized milk poses health risks without benefits

With disease outbreaks linked to unpasteurized milk rising in the United States, a review published in the January 1, 2009 issue of Clinical Infectious Diseases examines the dangers of drinking raw milk.

Milk and dairy products are cornerstones of a healthy diet. However, if those products are consumed unpasteurized, they can present a serious health hazard because of possible contamination with pathogenic bacteria. An average of 5.2 outbreaks per year linked to raw milk have occurred in the United States between 1993 and 2006—more than double the rate in the previous 19 years, according to co-authors Jeffrey T. LeJeune and Päivi J. Rajala-Schultz of the College of Veterinary Medicine in Columbus, Ohio. …

Raw milk advocates claim that unpasteurized milk cures or prevents disease, but no scientific evidence supports this notion. Testing raw milk, which has been suggested as an alternative to pasteurization, cannot ensure a product that is 100 percent safe and free of pathogens. Pasteurization remains the best way to reduce the unavoidable risk of contamination, according to the authors.

Pathogens in produce: a brief review

Following this morning’s report of a new European study demonstrating the potential for internalization of Salmonella in produce, Ben Chapman pulled together the following notes on the topic.

Irrigation water containing raw sewage or improperly treated effluents from sewage treatment plants may contain hepatitis A, Norwalk viruses, or enteroviruses in addition to bacterial pathogens such as E.coli O157:H7, Salmonella spp. and Shigella spp. (Beuchat, 1998).

Produce can also be contaminated with pathogens due to internalization of pathogens both through the root system and flesh or stem scars. Evidence of infiltration of bacteria into vegetables is reported in several articles (Bartz 1982; Bartz and Showalter 1981; Burnett et al., 2000; Seo and Frank 1999; Zhuang et al., 1995). Clear evidence exists to conclude that pathogens can be incorporated into fresh produce. So far, this evidence is based on laboratory experiments, not actual real world situations. Past research suggests that pathogens can enter lettuce plants through its roots and end up in the edible leaves. Small gaps in growing roots through which plant pathogens infect tissue may also allow E. coli entry (Solomon et al, 2002b; Warriner et al., 2003a, Warriner et al., 2003b).

The uptake of Salmonella spp. by roots of hydroponically grown tomato plants has been shown. Within one day of exposure to a high concentration mixture of Salmonella spp. pathogen cells were found in the hypocotyls, cotyledons, stems and leaves of young plants; though whether fruit is affected is not known at this time (Guo et al., 2002).

Solomon and colleagues (2002a) discovered that the transmission of E.coli O157:H7 to lettuce was possible through both spray and drip irrigation. They also found that the pathogen persisted on the plants for 20 days following application and submerging the lettuce in a solution of 200ppm chlorine did not eliminate all viable E.coli O157:H7 cells. This suggests that irrigation water of unknown microbial quality should be avoided in lettuce production (Solomon et al., 2002a).  In a follow-up experiment, Solomon and colleagues (2002b) explored the transmission of E. coli O157:H7 from manure-contaminated soil and irrigation water to lettuce plants. The researchers recovered viable cells from the inner tissues of the lettuce plants and found that the cells migrated to internal locations in plant tissue and were thus protected from the action of sanitizing agents These experiments demonstrated that E. coli O157:H7 can enter the lettuce plant through the root system and migrate throughout the edible portion of the plant (Solomon et al., 2002b).

The risk of contamination of produce due to Salmonella spp. was found to be increased when soil and water were present, and that soil and water actually act as reservoirs of the pathogen. Xuan and colleagues (2002) found that soil and water were factors in the infiltration of salmonella into the tissues of tomato. This supports the theory that preharvest contact with contaminated soil or water increased the contamination potential by certain pathogens and can lead to problems in pathogen removal and the efficacy of sanitizers.

Flesh scarring can provide a suitable environment for pathogen growth, and decreases the value of employing sanitizers, either in the packing shed or by consumers (Xuan et al., 2002).

The uptake of Salmonella spp. by roots of hydroponically grown tomato plants has also been shown. Within one day of exposure to a high concentration mixture of Salmonella spp. pathogen cells were found in the hypocotyls, cotyledons, stems and leaves of young plants; though whether fruit is affected is not known at this time (Guo et al., 2002).

In a 2006 review, Vectors and conditions for preharvest contamination of fruits and vegetables with  pathogens capable of causing enteric diseases,  Larry Beuchat of the Center for Food Safety and Department of Food Science and Technology at the University of Georgia, concluded:

"Manure, manure compost, sewage, sludge, irrigation water, and runoff water represent
avenues for introduction of pathogenic bacteria, parasites, and viruses to soil in which
fruits and vegetables intended to be eaten raw are grown. Pathogens vary in their
ability to survive in soil amendments and in soil. Inactivation rates and persistence in
soil are also influenced by soil type, rainfall, temperature, and agronomic practices.
Some pathogens can survive in soil for periods of time exceeding those needed to grow
plants from seeds or seedlings to the point of harvest. Pathogens originating from
preharvest environments may contaminate the surface of produce and evidence is
mounting that contamination of internal tissues can also occur. Prevention of
preharvest contamination of fruits and vegetables is an essential part of a systems
approach focused on applying interventions designed to achieve delivery of
microbiologically safe produce to the consumer."


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Bartz, J.A., and R.K. Showalter. 1981. Infiltration of tomatoes by aqueous bacterial suspensions. Phytopathology. 71: 515-518.

Beuchat, 2006. Vectors and conditions for preharvest contamination of fruits and vegetables with  pathogens capable of causing enteric diseases. British Food Journal 108 (1): 38-53.

Beuchat, L.R. 1998. Surface decontamination of fruits and vegetables eaten raw: a review. WHO/FSF/FOS/Publication 98.2. World Health Organization. Geneva. 49pp.

Burnett, S.L., Chen. J. and Beuchat, L.R. 2000. Attachment of Escherichia coli O157:H7 to the surfaces and internal structures of apples as detected by confocal scanning laser microscopy. Applied and Environmental Microbiology. 66: 4679-4687.

Guo, X., van Iersel, M. W., Chen, J., Brackett, R. E. and Beuchat, L. R. 2002. Evidence of association of salmonellae with tomato plants grown hydroponically in inoculated nutrient solution. Applied  Environmental Microbiology. 68: 3639-3643.

Hedberg, C.W., Angulo, F.J., White, K.E., Langkop, C.W., Schell, W.L., Stobierski M.G., Schuchat, A., Besser, J.M., Dietrich, S., Helsel, L., Griffin, P.M., McFarland J.W. and Osterholm M.T. 1999. Outbreaks of salmonellosis associated with eating uncooked tomatoes: implications for public health. Epidemiology and Infection 122: 385-93.

Seo, K. H., and J. F. Frank. 1999. Attachment of Escherichia coli O157:H7 to lettuce leaf surface and bacterial viability in response to chlorine treatment as demonstrated by using confocal scanning laser microscopy. Journal of Food Protection.  62: 3-9.

Solomon, E. B., Yaron, S., and Matthews, K.R. 2002b. Transmission of Escherichia coli O157:H7 from contaminated manure and irrigation water to lettuce plant tissue and its subsequent internalization. Applied Environmental Microbiology. 68: 397-400.

Solomon, E.B., ,Potenski, C.J. and Matthews, K.R. 2002a. Effect of irrigation method on transmission to and persistence of Escherichia coli O157:H7 on lettuce. Journal of Food Protection. 65: 673–676.

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Warriner K., Ibrahim F., Dickinson M,. Wright C. and Waites W.M. 2003b. Interaction of Escherichia coli with growing salad spinach plants. Journal of Food Protection. 66: 1790-1797.

Xuan, G., Jinru, C., Brackett, R.E., Beuchat, L.R. 2002. Survival of salmonella on tomatoes stored at high relative humidity, in soil, and on tomatoes in contact with soil. Journal of Food Protection. 65: 274-279.

Zhuang, R.-Y., Beuchat, L.R. and Angulo. F.J. 1995. Fate of Salmonella montevideo on and in raw tomatoes as affected by temperature and treatment with chlorine. Applied Environmental Microbiolology. 61: 2127-2131.