Yearly Archives: 2015

Whole genome sequencing finds listeria in unlikely places

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The listeria outbreak that killed three and prompted Texas ice cream company Blue Bell Creameries to recall every one of its products late last month is the latest example of how genetic epidemiology is changing the detection of foodborne illnesses.

whole.genome.sequencingTwo years ago, the U.S. Centers for Disease Control and Prevention (CDC) in Atlanta launched a pilot program to sequence the DNA of every listeria sample tied to an illness in the United States—all told, about 800 per year.

“Now that we’re turning whole-genome sequencing on, we’re identifying outbreak after outbreak,” says Brendan Jackson, a medical epidemiologist with CDC. “We’re also finding smaller outbreaks that we weren’t able to find before.” They’re also finding them originating in previously unsuspected foods, from caramel apples to ice cream.

The new detection method can identify gaps in the food safety system, especially when used alongside similar efforts by the Food and Drug Administration (FDA) to sequence samples from food and from the places where food is prepared, from factories to distribution centers, Jackson says. 

Whole-genome sequencing allows scientists to accurately compare every single DNA base pair in samples, giving them “a much sharper look at the differences and similarities in the strains,” Jackson says. The process takes longer—72 hours for testing compared with 48 hours—and it costs more. CDC’s goal is to create a national DNA database for foodborne pathogens from clinical samples that could be integrated with an already-existing FDA database of foodborne pathogens from food and environmental samples. The agency plans to add other foodborne illnesses, including salmonella and the most common disease-causing strain of Escherichia coli, to the project within 3 years.

It’s called a chlorine monitor: If you wash fresh produce, buy one

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Maintaining effective sanitizer concentration is of critical importance for preventing pathogen survival and transference during fresh-cut produce wash operation and for ensuring the safety of finished products. However, maintaining an adequate level of sanitizer in wash water can be challenging for processors due to the large organic load in the wash system.

tomato.dump.tankIn this study, we investigated how the survival of human pathogens was affected by the dynamic changes in water quality during chlorine depletion and replenishment in simulated produce washing operations. Lettuce extract was added incrementally into water containing pre-set levels of free chlorine to simulate the chlorine depletion process, and sodium hypochlorite was added incrementally into water containing pre-set levels of lettuce extract to simulate chlorine replenishment. Key water quality parameters were closely monitored and the bactericidal activity of the wash water was evaluated using three-strain cocktails of Escherichia coli O157:H7, Salmonella enterica, and Listeria monocytogenes. In both chlorine depletion and replenishment processes, no pathogen survival was observed when wash water free chlorine level was maintained above 3.66 mg/L, irrespective of the initial free chlorine levels (10, 50, 100 and 200 mg/L) or organic loading (chemical oxidation demand levels of 0, 532, 1013 and 1705 mg/L). At this free chlorine concentration, the measured ORP was 843 mV and pH was 5.12 for the chlorine depletion process; the measured ORP was 714 mV and pH was 6.97 for the chlorine replenishment process.

 This study provides quantitative data needed by the fresh-cut produce industry and the regulatory agencies to establish critical operational control parameters to prevent pathogen survival and cross-contamination during fresh produce washing.

 Inactivation dynamics of Salmonella enterica, Listeria monocytogenes, and Escherichia coli O157:H7 in wash water during simulated chlorine depletion and replenishment processes

Food Microbiology, Volume 50, September 2015, Pages 88–96

Bin Zhou, Yaguang Luo, Xiangwu Nou, Shuxia Lyu, Qin Wang

http://www.sciencedirect.com/science/article/pii/S0740002015000556

‘They should have been boiled’ 2 dead, 60 sick from Norovirus in frozen raspberries in Swedish retirement homes

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I didn’t think about it much until a couple of years ago, but now I boil all frozen berries.

frozen_raspberries(1)(1)Apparently that’s a good idea.

But sad that consumers have to be the critical control point.

Two people have died of suspected food poisoning and another hospitalized. Some 60 people have suffered food poisoning on several retirement homes in Ljungby municipality. The cause is believed to be the raspberries in a dessert.

The raspberries served at several retirement homes in Ljungby municipality boiled never – contrary to the recommendations contained.

“One should always boil the frozen foreign raspberries, says Elsie Castro, a molecular biologist at the National Public Health Agency.”

Mariana Axelsson, nutrition manager in Ljungby municipality, admits that the infected raspberries that caused an outbreak of Norwalk virus should have been cooked. The procedures have failed and will now be reviewed.

Hallonparfaiten served on several retirement homes in Ljungby and caused 60 people fell ill with Norwalk virus. Two elderly also have died , probably as a result of the disease.

Nosestretcher alert: beards are dirtier/have more poop than toilets

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Maybe I’m biased as a decade-long beard wearer but the clickbait trolling the Internet today about beard and bacteria isn’t the most science-based.
According to KOAT TV, one of the most venerable science publishing sources, microbiologist microbiologist John Golobic of Quest Diagnostics is concerned that a few  beards in the Albuquerque area are full of poop bacteria. Which ones, he doesn’t say. He’s heard saying ‘enterics’ in the video at the site. But that’s all we know about what is in beards. I look forward to the publication.zz-top
“I’m usually not surprised and I was surprised by this,” Golobic said.

Several of the beards that were tested contained a lot of normal bacteria, but some were comparable to toilets.

“Those are the types of things you’d find in (fecal matter),” Golobic said, referring to the tests.

Even though some of the bacteria won’t lead to illness, Golobic said it’s still a little concerning.

“There would be a degree of uncleanliness that would be somewhat disturbing,” Golobic said.

Golobic recommends a thorough beard scrubbing and lots of hand-washing.

“(Also), try to keep your hands away from your face, as much as possible,” he said.

If the city were to find similar samples in the water system, Golobic said it would need to be shut down for disinfecting (because it is an indicator in water – not in beards -ben).

 The headline likely has more poop in it than my beard does – without seeing the data.
The data isn’t there to ban beard wearers from food handling.

Foster Farms, regulators and a game of chicken

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Lynne Terry of The Oregonian writes in a comprehensive feature that over the course of a decade, hundreds of people from Eugene to Baker City to Portland and Seattle were struck by bouts of food poisoning so severe they fled to their doctors or emergency rooms for treatment.

chicken.south.parkThey had no idea what made them sick. But federal regulators did.

Oregon and Washington public health officials repeatedly told the U.S. Department of Agriculture they had linked salmonella outbreaks in 2004, 2009 and 2012 to Foster Farms chicken.

State officials pushed federal regulators to act, but salmonella-tainted chicken flowed into grocery stores, first in the Northwest, then across the country. Oregon investigators became so familiar with the culprit they gave it a name: the Foster Farms strain.

The outbreaks tied by state health officials to Foster Farms first occurred in Oregon and Washington. Then in 2012, illnesses spread to almost a dozen states. The next year, a new outbreak emerged that sickened more than 600 people across the country.

Much has been written about that last 16-month ordeal and the USDA’s slow response. But the way the federal agency handled it was not an isolated case, an investigation by The Oregonian/OregonLive has found.

Time after time dating to 2004, Oregon and Washington officials alerted the USDA’s food safety agency about salmonella illnesses, but the federal government chose not to warn the public or ask Foster Farms for a recall.

Foster-Farms-Chicken-BreastWith no reason to worry, people kept eating contaminated chicken.

Foster Farms processes hundreds of thousands of birds a day, and only a small fraction of its customers ever got sick.

But from 2004 through 2014, state or Centers for Disease Control and Prevention officials identified nearly 1,000 infections they said were linked to Foster Farms chicken in four separate outbreaks. About 300 of those cases occurred in Oregon and Washington. The overall toll was possibly much higher. The CDC estimates that for every confirmed salmonella infection, more than 29 go unreported.

The Oregonian/OregonLive reviewed thousands of pages of government records related to Foster Farms and interviewed dozens of health officials, inspectors, food safety experts and federal managers for this story. The records and interviews reveal for the first time an agency that over a 10-year span had repeatedly failed to protect consumers when confronting one of the nation’s largest poultry processors.

During that time, the USDA’s Food Safety and Inspection Service issued hundreds of citations at the company’s sprawling plant in Kelso, Washington. But the agency allowed the plant to operate even though people kept getting sick.

Since the last outbreak ended, no known illnesses have been tied to the company, the largest poultry processor in the West. Foster Farms says it now has one of the lowest salmonella rates in the industry, having invested tens of millions of dollars to improve its plants and procedures.

It’s a different story at the USDA.

The agency has boosted its food safety budget and has made some strides to protect consumers, including introducing stricter standards for salmonella and ordering more random tests.

But many of the same practices and cultural hurdles that contributed to the way the agency handled public health concerns during that 10-year span remain in place today.

chicken.shock.may.13USDA officials are so worried about being sued by companies that they’ve set a high bar for evidence, even rejecting samples of tainted chicken that state health agencies believed would help clinch their case, records and interviews show.

Union officials said the government inspectors they represent are pressured to go easy on food processors, citing one notable case in which the USDA transferred an inspector after Foster Farms complained he wrote too many citations. And after strong pushback from Foster Farms, the USDA retracted a reference in a public document that unequivocally linked the company to illnesses in 2004, a move that baffled state health officials who described the investigation as “rock solid.”

And there’s much more, including USDA’s unwritten rules for going public at http://www.oregonlive.com/usda-salmonella/#incart_m-rpt-1.

Food safety style: The art of the Japanese company apology

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Imagine you’re the head of a US fast-food chain in Japan that has been scandalized by a tooth-in-french-fries disaster. How do you repair the damage? Bow deeply — and be convincing.

belushi.samuriSo it was for Sarah Casanova, the Canadian president of McDonald’s Japan, whose less-than-textbook corporate mea culpa this month was an attempt at the tightly choreographed script routinely used by crisis-hit organisations.

With cameras rolling and reporters at the ready, apology press conferences are a must-do piece of theatre for Japanese firms that wandered from the straight-and-narrow in a country that has a dozen expressions for saying sorry.

Act 1: Wear dark colors, look grim and apologise profusely. Add a liberal sprinkling of words like “unfortunate” and “deeply regrettable”.

Act 2: Take a deep bow — better keep limber since you have got to make like a right angle or you will look like an amateur.

Act 3: Forget about buying a Porsche this year. You’ve got to cut your pay temporarily or forgo a bonus. Senior managers too.

Acts 4 and 5: Optional add-ons (depending on circumstances) — quit outright, or more likely step aside and put someone else in as CEO. Promise sweeping changes to avoid further scandals.

“This is part of a broader cultural phenomenon where the leader takes a hit for the team, then hopefully… society at large moves on,” says Jun Okumura, an independent analyst and visiting researcher at the Meiji Institute for Global Affairs.

Television and social media have made it all the more important to convince a Japanese public sensitive to visual cues, says Mitsuru Fukuda, a professor of crisis management and risk communications at Nihon University in Tokyo.

“A big difference is that in the West, facts matter,” he says.

“Japanese journalists… focus on top leaders’ apologies.”

Business communication specialist Yasuyuki Mogi adds: “Unless words of apology are at the forefront, many Japanese feel (it) lacks sincerity.”

But even a picture-perfect effort on Casanova’s part might not have helped much to make up for mounting losses and allay public concerns after a string of food scares, including the human tooth found in a box of french fries, says Jeff Kingston, a professor of Asian Studies at Temple University’s Tokyo campus.

“When you are in the business of selling food and your food is found wanting and considered unhealthy there is no bow low enough to right what is wrong.”

Blue Bell and fairytales about crisis communication

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Despite the angst surrounding Blue Bell Creameries’ well-publicized listeria outbreak, one thing is clear: Blue Bell has practiced stellar crisis communications.

listeria4No.

The company has been honest, transparent and accountable, qualities which have placed it in the best possible position to rebound from this crisis.

No.

Overwhelmingly, public response on Twitter has been positive. As one commenter put it: “I don’t think media quite understand the emotional attachment Texans feel for #BlueBell.”

I’m not sure the families of the three dead in Kansas would agree.

David Sommer, the Charles E. Cheever chair of risk management at St. Mary’s University said Blue Bell’s initial response has not been ideal, adding, “The multiple and expanding recalls kept the company in the news for six weeks. It’s important to get the facts out as soon as possible. A company must be seen as proactive, not reactive.”

Blue Bell has set up a toll-free telephone number for consumers to call with questions. It is 866-608-3940, according to its website. The Blue Bell website also has a statement from CEO and President Paul Kruse, dated April 20, that explains the company’s safety and testing steps that are now underway.

“The company will have to start a significant advertising campaign,” Sommer said. “It must have humility about its mistakes, apologize to its customers and add assurances that it won’t happen again.

“People want to know the company feels regret and is making assurances it won’t happen again.”

And to do that, with all the increased Listeria testing, make the results publicly available.

Don’t poop in the pool: Cryptosporidiosis surveillance, US 2011–2012

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Problem/Condition: Cryptosporidiosis is a nationally notifiable gastrointestinal illness caused by extremely chlorine-tolerant protozoa of the genus Cryptosporidium.

caddyshack.pool.poop-1Reporting Period: 2011–2012.

Description of System: Fifty state and two metropolitan public health agencies voluntarily report cases of cryptosporidiosis through CDC’s National Notifiable Diseases Surveillance System.

Results: For 2011, a total of 9,313 cryptosporidiosis cases (confirmed and nonconfirmed) were reported; for 2012, a total of 8,008 cases were reported; 5.8% and 5.3%, respectively, were associated with a detected outbreak. The rates of reported nonconfirmed cases were 1.0 and 0.9 per 100,000 population in 2011 and 2012, respectively, compared with an average of 0.0 during 1995–2004, and 0.3 during 2005–2010. The highest overall reporting rates were observed in the Midwest; 10 states reported >3.5 cases per 100,000 population in 2011 and in 2012. During 2011–2012, reported cases were highest among children aged 1–4 years (6.6 per 100,000 population), followed for the first time by elderly adults aged ≥80 years (3.4), and 75–79 years (3.3). Overall, cryptosporidiosis rates were higher among females than males during both years. For specific age groups, rates were higher among males than females aged <15 years and higher among females than males aged ≥15 years. Cryptosporidiosis symptom onset increased 4.4 fold during late summer.

Interpretation: Cryptosporidiosis incidence rates remain elevated nationally, and rates of nonconfirmed cases have increased. Rates remain highest in young children, although rates among elderly adults are increasing. Transmission of Cryptosporidium occurs throughout the United States, with increased reporting occurring in Midwestern states. Seasonal onset peaks coincide with the summer recreational water season and might reflect increased use of communal swimming venues.

Public Health Action: Future research is needed to address the evolving epidemiology of cryptosporidiosis cases, with a specific focus on the increase in nonconfirmed cases and increasing incidence rates among elderly adults. National systematic genotyping and subtyping of Cryptosporidium isolates could also help elucidate Cryptosporidium transmission and thus cryptosporidiosis epidemiology in the United States.

Beaver fever: Giardiasis surveillance, US 2011–2012

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Problem/Condition: Giardiasis is a nationally notifiable gastrointestinal illness caused by the protozoan parasite Giardia intestinalis.

Reporting Period: 2011–2012.

beaver.feverDescription of System: Forty-four states, the District of Columbia, New York City, the Commonwealth of Puerto Rico, and Guam voluntarily reported cases of giardiasis to CDC through the National Notifiable Diseases Surveillance System (NNDSS).

Results: For 2011, a total of 16,868 giardiasis cases (98.8% confirmed and 1.2% nonconfirmed) were reported; for 2012, a total of 15,223 cases (98.8% confirmed and 1.3% nonconfirmed) were reported. In 2011 and 2012, 1.5% and 1.3% of cases, respectively, were associated with a detected outbreak. The incidence rates of all reported cases were 6.4 per 100,000 population in 2011 and 5.8 per 100,000 population in 2012. This represents a slight decline from the relatively steady rates observed during 2005–2010 (range: 7.1–7.9 cases per 100,000 population). In both 2011 and 2012, cases were most frequently reported in children aged 1–4 years, followed by those aged 5–9 years and adults aged 45–49 years. Incidence of giardiasis was highest in Northwest states. Peak onset of illness occurred annually during early summer through early fall.

Interpretation: For the first time since 2002, giardiasis rates appear to be decreasing. Possible reasons for the decrease in rates during 2011–2012 could include changes in transmission patterns, a recent change in surveillance case definition, increased uptake of strategies to reduce waterborne transmission, or a combination of these factors. Transmission of giardiasis occurs throughout the United States, with more frequent diagnosis or reporting occurring in northern states. Geographical differences might suggest actual regional differences in giardiasis transmission or variation in surveillance capacity across states. Six states did not report giardiasis cases in 2011–2012, representing the largest number of nonreporting states since giardiasis became nationally notifiable in 2002. Giardiasis is reported more frequently in young children, which might reflect increased contact with contaminated water or ill persons, or a lack of immunity.

Public Health Action: Educational efforts to decrease exposure to unsafe drinking and recreational water and prevent person-to-person transmission have the potential to reduce giardiasis transmission. The continual decrease in jurisdictions opting to report giardiasis cases could negatively impact the ability to interpret national surveillance data; thus, further investigation is needed to identify barriers to and facilitators of giardiasis case reporting. Existing state and local public health infrastructure supported through CDC (e.g., Epidemiology and Laboratory Capacity grants and CDC-sponsored Council of State and Territorial Epidemiologists Applied Epidemiology Fellows) could provide resources to enhance understanding of giardiasis epidemiology.