European Food Safety Authority: Update on Salmonella agona outbreak

The withdrawal and/or recall of infant formula produced by a single French processing company will significantly reduce the risk of more infants being infected by Salmonella Agona, say EFSA and ECDC as a result of a rapid outbreak assessment.

An outbreak of S. Agona linked to the consumption of infant formula has been ongoing in France since August 2017. So far the outbreak has affected 37 children under one year of age in France. Whole genome sequencing (WGS) analysis confirmed that a Spanish case is closely related to the outbreak in France. A probable case has been identified in Greece. The last case was notified on 2 December 2017.

EFSA and ECDC recommend that competent authorities in affected Member States keep sharing information on the epidemiological, microbiological and environmental investigations and issue relevant notifications in the Rapid Alert System for Food and Feed (RASFF) and the Early Warning Response System (EWRS).

To prevent infections using infant formulas, both in infants and caregivers, Member States should consider providing advice to the public regarding:

Not to use any of the infant formulas involved in this outbreak;

Hand washing before and after the preparation of the bottle;

Bottles should not be prepared in advance and the contents should be discarded if not consumed within two hours.

What is a rapid outbreak assessment?

In case of multi-country foodborne outbreaks coordination at EU level is important. A Rapid Outbreak Assessment is jointly prepared by EFSA and ECDC in close cooperation with affected countries. The ROA gives an overview of the situation in terms of public health and identifies the contaminated food vehicle that caused the infections. It also includes trace-back and trace-forward investigations to identify the origin of the outbreak and where contaminated products have been distributed. This is crucial to identify the relevant control measures in order to prevent further spread of the outbreak.

An outbreak of Salmonella Agona linked to the consumption of infant formula (powdered milk) has been ongoing in France since August 2017. As of 11 January 2018, the outbreak had affected 39 infants (children <1 year of age): 37 in France, one in Spain confirmed by whole genome sequencing (WGS) and one in Greece, considered to be associated with this event based on the presence of a rare biochemical characteristic of the isolate.

The date of symptom onset for the most recent case was 2 December 2017. Available evidence from epidemiological investigations in humans and traceability investigations in food identified seven different brands of infant formula from a single processing company in France as the vehicles of infection.

After receiving the first notification on 2 December 2017 of an unusual number of S. Agona cases in France, the French authorities carried out investigations at the implicated factory. On 4 December 2017, they notified the Rapid Alert System for Food and Feed (RASFF) after confirming that some of the affected products were exported to other countries. Following investigations at the processing company, all products manufactured since 15 February 2017, including products other than infant formula, have been recalled and/or withdrawn, as a precautionary measure. The French competent authorities are verifying that the measures taken by the processing company in response to this event have been sufficient and appropriate. As of 15 January 2018, recalled products had been distributed to 13 European Union (EU) countries (Belgium, Bulgaria, Cyprus, the Czech Republic, France, Greece, Ireland, the Netherlands, Romania, Slovenia, Slovakia, Spain and the United Kingdom) and to 54 third countries. Most of the batches involved in the investigation have not yet passed their expiry date. However, broad withdrawal and/or recall measures, export bans and a suspension of market distribution of these batches, implemented since the beginning of December 2017 by the French competent authority and processing company A, are likely to significantly reduce the risk of human infection. The possibility remains, however, that new cases may be detected. Third countries, where the recalled products had been distributed, have been notified by RASFF through INFOSAN. ECDC offers WGS services to EU/EEA countries that do not have the capacity for a timely sequencing and analysis as part of this investigation. A multi-country WGS analysis is under way at the Pasteur Institute.

Whole genome sequencing is just a technique, with pros and cons: Australia still has a (raw) egg problem

In Australia, the incidence of Salmonella Typhimurium has increased dramatically over the past decade. Whole-genome sequencing (WGS) is transforming public health microbiology, but poses challenges for surveillance.

To compare WGS-based approaches with conventional typing for Salmonella surveillance, we performed concurrent WGS and multilocus variable-number tandem-repeat analysis (MLVA) of Salmonella Typhimurium isolates from the Australian Capital Territory (ACT) for a period of 5 months. We exchanged data via a central shared virtual machine and performed comparative genomic analyses. Epidemiological evidence was integrated with WGS-derived data to identify related isolates and sources of infection, and we compared WGS data for surveillance with findings from MLVA typing.

We found that WGS data combined with epidemiological data linked an additional 9% of isolates to at least one other isolate in the study in contrast to MLVA and epidemiological data, and 19% more isolates than epidemiological data alone. Analysis of risk factors showed that in one WGS-defined cluster, human cases had higher odds of purchasing a single egg brand. While WGS was more sensitive and specific than conventional typing methods, we identified barriers to uptake of genomic surveillance around complexity of reporting of WGS results, timeliness, acceptability, and stability.

In conclusion, WGS offers higher resolution of Salmonella Typhimurium laboratory surveillance than existing methods and can provide further evidence on sources of infection in case and outbreak investigations for public health action. However, there are several challenges that need to be addressed for effective implementation of genomic surveillance in Australia.

Incorporating whole-genome sequencing into public health surveillance: Lessons from prospective sequencing of salmonella typhimurium in Australia

16 January 2018

Foodborne Pathogens and Disease

Laura Ford, Glen Carter, Qinning Wang, Torsten eemann, Vitali Sintchenko, Kathryn Glass, Deborah Williamson, Peter Howard, Mary Valcanis, Cristina Castillo, Michelle Sait, Benjamin Howden, and Martyn Kirk

https://doi.org/10.1089/fpd.2017.2352

http://online.liebertpub.com/doi/abs/10.1089/fpd.2017.2352

 

Cilantro has a history of shits: Produce risk modelling in India

This study estimates illness (diarrhea) risks from fecal pathogens that can be transmitted via fecal-contaminated fresh produce. To do this, a quantitative microbial risk assessment (QMRA) framework was developed in National Capital Region, India based on bacterial indicator and pathogen data from fresh produce wash samples collected at local markets.

Produce wash samples were analyzed for fecal indicator bacteria (Escherichia coli, total Bacteroidales) and pathogens (Salmonella, Shiga-toxin producing E. coli (STEC), enterohemorrhagic E. coli (EHEC)). Based on the E. coli data and on literature values for Cryptosporidium and norovirus, the annual mean diarrhea risk posed by ingestion of fresh produce ranged from 18% in cucumbers to 59% in cilantro for E. coli O157:H7, and was <0.0001% for Cryptosporidium; for norovirus the risk was 11% for cucumbers and up to 46% for cilantro. The risks were drastically reduced, from 59% to 4% for E. coli O157:H7, and from 46% to 2% for norovirus for cilantro in post-harvest washing and disinfection scenario.

The present QMRA study revealed the potential hazards of eating raw produce and how post-harvest practices can reduce the risk of illness. The results may lead to better food safety surveillance systems and use of hygienic practices pre- and post-harvest.

Quantitative microbial risk assessment to estimate the risk of diarrheal diseases from fresh produce consumption in India

Food Microbiology, January 2018

Arti Kundu, Stefan Wuertz, Woutrina Smith

DOI: 10.1016/j.fm.2018.01.017 

http://www.x-mol.com/paper/530702

Jimmy Johns linked to sprout outbreak again

I can’t remember if this is outbreak number 3 or 4 (oops, it’s number 5 according to the Chicago Tribune) but Jimmy Johns, the sub folks, have been linked to a bunch of salmonellosis illnesses through sprouts again.

I wonder if their PR folks regret this sprout marketing ploy (right, exactly as shown) from a few years ago. Skull. Crossbones. Eat at your own risk. Nudge. Nudge. Say no more.

Yeah. And there are illnesses again.

“Food safety and the welfare of our customers are our top priorities and not negotiable in our business,” said James North, Jimmy John’s President and CEO, in a news release, adding the company is working with the various agencies in the investigation.

Here’s a table of over 75 sprout-related outbreaks going back to 1973. We’ll add this one when there are more details.

Nudge. Nudge.

 

Modeling to reduce risks of Salmonella in alfalfa sprouts

We developed a risk assessment of human salmonellosis associated with consumption of alfalfa sprouts in the United States to evaluate the public health impact of applying treatments to seeds (0–5-log10 reduction in Salmonella) and testing spent irrigation water (SIW) during production.

The risk model considered variability and uncertainty in Salmonella contamination in seeds, Salmonella growth and spread during sprout production, sprout consumption, and Salmonella dose response.

Based on an estimated prevalence of 2.35% for 6.8 kg seed batches and without interventions, the model predicted 76,600 (95% confidence interval (CI) 15,400–248,000) cases/year. Risk reduction (by 5- to 7-fold) predicted from a 1-log10 seed treatment alone was comparable to SIW testing alone, and each additional 1-log10 seed treatment was predicted to provide a greater risk reduction than SIW testing. A 3-log10 or a 5-log10 seed treatment reduced the predicted cases/year to 139 (95% CI 33–448) or 1.4 (95% CI <1–4.5), respectively. Combined with SIW testing, a 3-log10 or 5-log10 seed treatment reduced the cases/year to 45 (95% CI 10–146) or <1 (95% CI <1–1.5), respectively. If the SIW coverage was less complete (i.e., less representative), a smaller risk reduction was predicted, e.g., a combined 3-log10 seed treatment and SIW testing with 20% coverage resulted in an estimated 92 (95% CI 22–298) cases/year.

Analysis of alternative scenarios using different assumptions for key model inputs showed that the predicted relative risk reductions are robust. This risk assessment provides a comprehensive approach for evaluating the public health impact of various interventions in a sprout production system.

Risk assessment of salmonellosis from consumption of alfalfa sprouts and evaluation of the public health impact of sprout seed treatment and spent irrigation water testing

January 2018, Risk Analysis

Yuhuan Chen, Regis Pouillot, Sofia Farakos, Steven Duret, Judith Spungen, Tong-Jen Fu, Fazila Shakir, Patricia Homola, Sherri Dennis, Jane Van Doren

DOI: 10.1111/risa.12964

http://onlinelibrary.wiley.com/doi/10.1111/risa.12964/epdf

26 sick: Multistate outbreak of Salmonella infections linked to Coconut Tree brand frozen shredded coconut

The U.S. Centers for Disease Control (CDC), public health and regulatory officials in several states, and the U.S. Food and Drug Administration (FDA) are investigating a multistate outbreak of Salmonella infections.

As of January 12, 2018, 25 people infected with the outbreak strains of Salmonella I 4,[5],12:b:- (24 people) or Salmonella Newport (1 person) have been reported from 9 states. One more ill person infected with the outbreak strain of Salmonella I 4,[5],12:b:- has been reported from Canada.

WGS showed that isolates from people infected with Salmonella I 4,[5],12:b:- are closely related genetically. This close genetic relationship means that people in this outbreak are more likely to share a common source of infection.

Illnesses started on dates ranging from May 11, 2017 to November 4, 2017. Ill people range in age from 1 year to 82, with a median age of 19. Among ill people, 19 (76%) are male. Six people (24%) report being hospitalized. No deaths have been reported.

Epidemiologic, laboratory, and traceback evidence indicates that Coconut Tree Brand frozen Shredded Coconut is the likely source of this multistate outbreak. This investigation is ongoing.

In interviews, ill people answered questions about the foods they ate and other exposures in the week before they became ill. Ten (63%) of 16 people interviewed reported eating or maybe eating coconut. Of these 10 people, 8 (80%) reported having an Asian-style dessert drink that contained frozen shredded coconut.

Throughout the outbreak investigation, state and local health officials have collected different food items from restaurants where ill people consumed Asian-style dessert drinks. In November 2017, laboratory testing of a sample from coconut milk made in one restaurant in New York did not identify the outbreak strain of Salmonella I 4,[5],12:b:-, but did identify a strain of SalmonellaNewport. This sample was from coconut milk made with Coconut Tree Brand frozen Shredded Coconut, as well as other ingredients. WGS showed that the Salmonella Newport isolated from the coconut milk was closely related genetically to a Salmonella Newport isolate from an ill person from Massachusetts who had consumed an Asian-style dessert drink.

In December 2017, officials in Massachusetts collected food items from a restaurant where that ill person had consumed Asian-style dessert drinks. One sample from frozen shredded coconut identified a strain of Salmonella that was new to the PulseNet database and has not been linked to any illnesses. This sample was from an unopened package of Coconut Tree Brand Frozen Shredded Coconut. As a result, on January 3, 2018, Evershing International Trading Company recalled all Coconut Tree Brand Frozen Shredded Coconut. The recalled product was packaged in 16-ounce plastic bags.

Officials in Massachusetts returned to the restaurant and collected more Coconut Tree Brand frozen Shredded Coconut in January 2018. On January 12, laboratory testing confirmed that samples from that frozen shredded coconut identified the outbreak strain of Salmonella I 4,[5],12:b:-. Laboratory testing of other samples identified several types of Salmonella bacteria, including Salmonella Javiana, Salmonella Rissen, and Salmonella Thompson. These samples were from unopened packages of Coconut Tree Brand Frozen Shredded Coconut sold before January 3, 2018. CDC is reviewing the PulseNet database to determine if the other Salmonella isolates from the frozen shredded coconut are linked to any illnesses.

Frozen shredded coconut can last for several months if kept frozen and may still be in retail stores or in people’s homes. CDC recommends that retailers not sell, restaurants not serve, and consumers not eat recalled Coconut Tree Brand frozen Shredded Coconut.

Salmonella may have caused a massive Aztec epidemic, study finds

Rebecca Hersher of NPR reports that in 1545, people in the Mexican highlands starting dying in enormous numbers. People infected with the disease bled and vomited before they died. Many had red spots on their skin.

It was one of the most devastating epidemics in human history. The 1545 outbreak, and a second wave in 1576, killed an estimated 7 million to 17 million people and contributed to the destruction of the Aztec Empire.

But identifying the pathogen responsible for the carnage has been difficult for scientists because infectious diseases leave behind very little archaeological evidence.

“There have been different schools of thought on what this disease was. Could it have been plague? Could it have been typhoid fever? Could it have been a litany of other diseases?” says Kirsten Bos, a molecular paleopathologist at the Max Planck Institute in Germany, and an author of a new study published Monday in Nature Ecology and Evolution.

The study analyzes DNA from the teeth of 10 people who died during the epidemic and pinpoints a possible culprit: a type of salmonella that causes a deadly fever.

A new algorithm allowed Bos and her team to identify fragments of ancient salmonella DNA with extreme specificity.

“It was an analytical technique that was really the game-changer for us,” Bos explains. While scientists have been able to extract ancient DNA from bones and other tissue, until recently it was impossible to compare that extracted DNA to a wide variety of potential matches.

But a new computer program called MALT allowed them to do just that. “The major advancement was this algorithm,” Bos says. “It offers a method of analyzing many, many, many small DNA fragments that we get, and actually identifying, by species name, the bacteria that are represented.”

Bos and her team used MALT to match up the DNA fragments extracted from teeth of epidemic victims with a database of known pathogens. The program didn’t entire save them from mind-numbing work — at one point PhD student and study author Ashild Vagene had to go through the results of the program by hand.

In the end, they found evidence of the deadly Salmonella enterica Paratyphi C bacteria.

The study does not pinpoint the source of the bacteria, which is an area of great interest for biologists and archaeologists alike. The authors note that many epidemics of the period are believed to originate with European invaders who arrived in the region in the early part of the 16th century, but the new research doesn’t present biological evidence for or against that.

Salmonella enterica gemones from victims of a major sixteenth-century epidemic in Mexico

Nature Ecology and Evolution, Published online 15 January 2018, Åshild J. VågeneAlexander HerbigMichael G. CampanaNelly M. Robles GarcíaChristina WarinnerSusanna SabinMaria A. SpyrouAida Andrades ValtueñaDaniel HusonNoreen TurossKirsten I. Bos & Johannes Krause, doi:10.1038/s41559-017-0446-6

https://www.nature.com/articles/s41559-017-0446-6

Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown.

Through the introduction of a new metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked, based on historical and archaeological evidence, to the 1545–1550 CE epidemic that affected large parts of Mexico. Locally, this epidemic was known as ‘cocoliztli’, the pathogenic cause of which has been debated for more than a century.

Here, we present genome-wide data from ten individuals for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.

36 sick: Lactalis offers salmonella compensation, French government says probe continues

We’re in New Caledonia for Amy to do some French professoring stuff, with the Calgary-Carolina hockey game on in the background on a sports channel from France.

I went for a walk along the ocean this morning, sans Ted, which is the extent of my French.

While I’m surrounded by the beauty of this Pacific island, the Lactalis mess in France continues a downslide into parody (except for the sick kids and their families).

According to Reuters, France welcomed dairy group Lactalis’ pledge to compensate victims of a Salmonella contamination in its baby milk on Sunday, but said a judicial investigation to determine who was responsible would continue.

Lactalis Chief Executive Emmanuel Besnier told the weekly Journal du Dimanche his family company, one of the world’s biggest dairies, would “pay damages to every family which has suffered a prejudice.”

Is prejudice French for barfing?

Salmonella infections can be life-threatening and the families of three dozen children who have fallen sick in France as a result of the contaminated baby milk have announced a raft of lawsuits.

Besnier’s promise came two days after Lactalis widened a product recall to cover all infant formula made at its Craon plan, regardless of the manufacture date, in a bid to contain the fallout from a health scare that risks damaging France’s strategic agribusiness in overseas markets.

“Paying compensation is good, but money cannot buy everything,” government spokesman Benjamin Griveaux said in an interview on BFM TV.

The health scare intensified last week after France’s biggest retailers including Carrefour, Auchan and Leclerc admitted products recalled in December had still found their way onto shelves.

“It is the job of the investigation to determine where failings occurred and who is to blame,” Griveaux said, adding that “responsibilities were shared.”

Implementing the global recall will be challenging. Privately owned Lactalis, one of the world’s biggest dairies, exports its baby food products to 83 countries across Europe, Africa and Asia.

The recall involves some 12 million tins of baby milk.

“It’s not easy to evaluate the number of items that need to be returned because we don’t know what’s been consumed already,” Besnier said in a rare newspaper interview published on Sunday.

Friday’s recall was the third in a month and Lactalis has come under fire for its clumsy response. Besnier also told the French weekly that the company had acted as quickly and efficiently as possible and denied slowing the process to curb losses.

Besnier has also been criticized for failing to speak out publicly during the salmonella scare.

While his family are France’s 11th wealthiest, according to a 2017 ranking by Challenges magazine, the dairy tycoon has long shunned the public limelight and schmoozing with politicians.

His workers nickname him the “invisible man.”

“We’re a discreet business. In this region there is a mentality of ‘work first, speak later,” he said. But he acknowledged lessons had been learned during the past few weeks.

Lactalis has become an industry giant, with annual sales of 17 billion euros ($20.73 billion) and 18,900 employees across some 40 countries.


 

Looks like Chile has an egg problem: 174 sick with Salmonella linked to homemade mayo

The Bío Bío Department of Health has confirmed 174 cases of salmonellosis in people who consumed homemade mayonnaise in the local “Dulce y Salado” (“Sweet and Salty”) of Lota.

Among those affected are 25 hospitalized for severe dehydration, including a pregnant woman. There are also sufferers of all ages, such as a one-year-old baby and up to an adult older than 91.
According to the health authority, the number of patients should not increase substantially due to the number of days that have passed since the closure of the premises, on Jan. 3. 2018. Now it is expected that laboratories in Santiago will determine the serotype of the strain, which may allow them to fully define whether the raw egg was responsible for this outbreak.

 

Whole genone sequencing fingers ham as source of Salmonella outbreak in Netherlands

In January 2017, an increase in reported Salmonella enterica serotype Bovismorbificans cases in the Netherlands was observed since October 2016. We implemented a case–control study to identify the source, including all cases after December 2016.

Adjusted odds ratios were calculated using logistic regression analysis. We traced back the distribution chain of suspected food items and sampled them for microbiological analysis. Human and food isolates were sequenced using whole genome sequencing (WGS).

From October 2016 to March 2017, 54 S. Bovismorbificans cases were identified. Sequencing indicated that all were infected with identical strains. Twenty-four cases and 37 controls participated in the study. Cases were more likely to have consumed ham products than controls (aOR = 13; 95% CI: 2.0–77) and to have shopped at a supermarket chain (aOR = 7; 95% CI: 1.3–38).

Trace-back investigations led to a Belgian meat processor: one retail ham sample originating from this processor tested positive for S. Bovismorbificans and matched the outbreak strain by WGS. All ham products related to the same batch were removed from the market to prevent further cases. This investigation illustrates the importance of laboratory surveillance for all Salmonella serotypes and the usefulness of WGS in an outbreak investigation.

Outbreak of Salmonella Bovismorbificans associated with the consumption of uncooked ham products, the Netherlands, 2016 to 2017

Eurosurveillance; Volume 23; Issue 1; 4 January 2018

Brandwagt Diederik, van den Wijngaard Cees, Tulen Anna Dolores, Mulder Annemieke Christine, Hofhuis Agnetha, Jacobs Rianne, Heck Max, Verbruggen Anjo, van den Kerkhof Hans, Slegers-Fitz-James Ife, Mughini-Gras Lapo, Franz Eelco

http://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2018.23.1.17-00335