Rise of the machines: Tools to know if Salmonella will hit your livestock

Increasingly, routine surveillance and monitoring of foodborne pathogens using whole-genome sequencing is creating opportunities to study foodborne illness epidemiology beyond routine outbreak investigations and case–control studies.

Using a global phylogeny of Salmonella enterica serotype Typhimurium, we found that major livestock sources of the pathogen in the United States can be predicted through whole-genome sequencing data. Relatively steady rates of sequence divergence in livestock lineages enabled the inference of their recent origins.

Elevated accumulation of lineage-specific pseudogenes after divergence from generalist populations and possible metabolic acclimation in a representative swine isolate indicates possible emergence of host adaptation.

We developed and retrospectively applied a machine learning Random Forest classifier for genomic source prediction of Salmonella Typhimurium that correctly attributed 7 of 8 major zoonotic outbreaks in the United States during 1998–2013. We further identified 50 key genetic features that were sufficient for robust livestock source prediction.

Zoonotic source attribution of Salmonella enterica serotype Typhimurium using genomic surveillance data, United States

Emerging Infectious Diseases vol. 25 no. 1

Shaokang Zhang, Shaoting Li, Weidong Gu, Henk den Bakker, Dave Boxrud, Angie Taylor, Chandler Roe, Elizabeth Driebe, David M. Engelthaler, Marc Allard, Eric Brown, Patrick McDermott, Shaohua Zhao, Beau B. Bruce, Eija Trees, Patricia I. Fields, and Xiangyu Deng 

We don’t need no edumacation

For all the folks out there trying to educate consumers and others about food safety, forget it.

Stick with stories.

Pink Floyd figured that out in 1980, in what would become the soundtrack for my grade 12 (Stones’ Some Girls was the soundtrack for grade 10) and a weirdly accurate foretelling of my first marriage.

Is there anybody out there? Physicians and handwashing

Our objectives were to evaluate the utility of electronic hand hygiene counting devices in outpatient settings and the impact of results feedback on physicians’ hand hygiene behaviors.

big-brother-1984We installed 130 electronic hand hygiene counting devices in our redesigned outpatient department. We remotely monitored physicians’ hand hygiene practices during outpatient examinations and calculated the adherence rate as follows: number of hand hygiene counts divided by the number of outpatients examined multiplied by 100. Physician individual adherence rates were also classified into 4 categories.

Results

Two hundred and eighty physicians from 28 clinical departments were monitored for 3 months. The overall hand hygiene adherence rate was 10.7% at baseline, which improved significantly after feedback to 18.2% in the third month. Of the clinical departments, 78.6% demonstrated significant improvement in hand hygiene compliance. The change in the percentage of physicians in each category before and after feedback were as follows: very low (84.3% to 72.1%), low (8.6% to 14.3%), moderate (2.9% to 8.9%), and high (4.3% to 4.6%), from the first to third month, respectively. Based on category assessment, 17.1% of physicians were classified as responders.

Conclusions

Physicians’ adherence to hand hygiene practices during outpatient examinations was successfully monitored remotely using electronic counting devices. Audit and feedback of adherence data may have a positive impact on physicians’ hand hygiene compliance.

Utility of electronic hand hygiene counting devices for measuring physicians’ handwashing

American Journal of Infection Control, DOI: http://dx.doi.org/10.1016/j.ajic.2016.08.002

A Arai, M Tanabe, A Nakamura, D Yamasaki, Y Muraki, T Kaneko, A Kadowaki, M Ito

http://www.sciencedirect.com/science/article/pii/S0196655316307532

 

No cause IDed, but UK children told to get back to class after E. coli outbreak

There were 71 pupils absent at Carlogie Primary on Monday which was a fifth of the school roll of 346 with 46 being kept off as a precaution.

On Tuesday 57 were absent with 37 kept off as a precaution.

A spokesman for Angus Council said: “Members of the community are understandably concerned and have provided tremendous support in trying to minimise spread of infection and identify a possible source.

“The cases and contacts have now been identified and children should now be attending school or nursery unless they are symptomatic or have been formally excluded by the Health Protection Team.”

Part of Tayside Children’s Hospital at Ninewells in Dundee has been set aside for confirmed and suspected cases in the Angus E. coli O157 outbreak.

NHS Tayside confirmed the move as part of what health chiefs described as an “evolving situation” in which a young girl also remains seriously ill in a Glasgow hospital.

The Peter Pan playgroup at the centre of the Angus investigation remains closed.

On the toilet 30X a day: UK couple’s Mexico holiday hell after contracting Cyclospora

Tony Larner of the Mirror reports a British couple’s dream Mexican holiday was left in tatters after they were struck down Cyclospora.

hanging.on.in.quiet.desperationSandra and Lee Harper splashed out £3,700 on an all-inclusive Thomson break to Riviera Maya resort, near Cancun.

But the couple, from Birmingham, were unable to leave their room for almost a week after falling ill with Cyclospora and needing the toilet up to 30 times every day.

The pair claim they complained about their illness and hygiene issues at their hotel to Thomson, but did not got a reply until after they arrived home, the Birmingham Mail reported.

UK Health officials have issued warnings about visiting the area after almost 100 Brits were struck down with the bug since the outbreak began in June.

A spokesthingy for Thomson said: “Public Health England has advised us of a number of sickness cases associated to an issue called Cyclospora in the Riviera Maya region of Mexico.”

An issue called Cyclospora?

“Hanging on in quiet desperation is the English way.”

Another brick in the wall: schools don’t want no pink slime

AP reports U.S. school districts are turning up their noses at pink slime, the beef product that caused a public uproar earlier this year.

The U.S. Department of Agriculture says the vast majority of states participating in its National School Lunch Program have opted to order ground beef that doesn’t contain the product known as lean finely textured beef.

Only three states – Iowa, Nebraska and South Dakota – chose to order beef that may contain the filler.

But as of May 18, the agency says states ordered more than 20 million pounds of ground beef products that don’t contain lean finely textured beef. Orders for beef that may contain the filler came to about 1 million pounds.

Doctors work while sick: study

People shouldn’t work preparing or serving food when they are sick because they may spread the illness. That’s become a food safety mantra, and yet outbreaks are repeatedly traced back to sick food workers – like the 300 who got sick with norovirus at the Haaaaarvard faculty club earlier this year after 14 food service employees were discovered to be working while sick. Or the 529 who got sick with norovirus at Heston Blumenthal’s Fat Duck restaurant last year, where again, the presence of sick food workers was cited as a contributing factor to the outbreak.

There’s a difference between saying what should be done – sick workers stay at home – and actually doing it – food service workers may get fired, whether they work with divas or in dives.

Medical doctors are the same.

The Associated Press reports more than half of doctors in training said in a survey that they’d shown up sick to work, and almost one-third said they’d done it more than once.

Dr. Anupam Jena, a medical resident at Massachusetts General Hospital in Boston, developed food poisoning symptoms halfway through an overnight shift last year, but said he didn’t think he was contagious or that his illness hampered his ability to take care of patients.

Jena, a study co-author, said getting someone else to take over his shift on short notice "was not worth the cost of working while a bit sick." He was not among the survey participants.

The researchers analyzed an anonymous survey of 537 medical residents at 12 hospitals around the country conducted last year by the Accreditation Council for Graduate Medical Education. The response rate was high; the hospitals were not identified.

The results appear in Wednesday’s Journal of the American Medical Association.

Nearly 58 percent of the respondents said they’d worked at least once while sick and 31 percent said they’d worked more than once while sick in the previous year.

Food service workers unite: Pink Floyd wins court battle with EMI over downloads

The British rock band Pink Floyd, a favorite for North American food service workers, won its court battle with EMI on Thursday, with a ruling that prevents the record company from selling single downloads on the Internet from the group’s concept albums.

Is that good or bad for restaurant back kitchens across the nation? The tune, Time, holds up well on its own, but the band wants the listener to experience the entire Dark Side of the Moon experience, which was fairly groovy when it came out in the 1970s, but a little dated, slow and self-indulgent today.

And who says rock’n roll is about attitude. Pink Floyd’s body of work is a coveted commodity. The band members Roger Waters, David Gilmour and Nick Mason all appeared on the 2009 Sunday Times Rich List with personal fortunes estimated at £85 million, £78 million and £50 million respectively.

Pink Floyd and Fargo Rock City: food service and music

PhD student Ben Chapman went and worked in a restaurant as part of his food safety research. He saw lots of things, but his most memorable description of kitchen work was that he had to listen to a lot of Pink Floyd.

There was some Tom Petty, and The Clash, but a lot of Pink Floyd. So it was with a nod and a lighter raised in the air to food service workers everywhere upon hearing the nears that founding Floyd keyboardist Richard Wright passed today.

But Pink Floyd doesn’t get much airplay in the Midwest. For a full accounting of why the Midwest is home to terrible hair metal, check out Chuck Klosterman’s Fargo Rock City, which Chapman loaned me a couple of years ago. And today, a barfblog reader e-mailed me to say,

“What I find most amusing about these Listeria posts is the album cover from the (very horrible and untalented) metal band.”
 
A few e-mails later, and she says,

“There is at least one metal band for every disease, especially those involving vomit, blood, decay, puss, gangreen or amptutation.

“I just found ascaris, a death metal band in denver.  i think this should be an ongoing theme – each post should have an accompanying death metal promotion."

But the best was when she linked me to a Strongbad post – Amy’s been a fan for years – about cliché metal bands. The comments section of barfblog.com is developing nicely.