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

 

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.

 

10 family members sick with Salmonella in Israel: Probably raw egg mousse

The Yeshiva World reports that 10 family members, adults and children, visited the emergency room of Mayanei HaYeshua Hospital in Bnei Brak on Monday, 7 Teves, presenting with severe intestinal illness. Three of them were hospitalized in the pediatric ward. The illness began after eating homemade mousse prepared from raw eggs.

The microbiological laboratory at the hospital identified the suspicious growth as salmonella and tomorrow, Tuesday, the suspicions of doctors will be confirmed. For the time being, the family is ill and suffering.

Does Europe have an egg problem? Salmonella cases no longer falling in the EU

The declining trend of salmonellosis cases in the EU has levelled off according to the annual report on zoonotic diseases published today.

The European Centre for Disease Prevention and Control reports that cases of Salmonella Enteritiis acquired in the EU have increased in humans by 3% since 2014. In laying hens, the prevalence increased from 0.7% to 1.21% over the same period. 

“The increase shown by our surveillance data is worrying and a reminder that we have to stay vigilant,” said Mike Catchpole, ECDC’s Chief Scientist. “Even in a state of high awareness and with national control programmes for S. Enteritidis in place, there is a need for continuing risk management actions at the Member State and EU level,” he added. 

Marta Hugas, EFSA’s Chief Scientist, said: “The decrease of Salmonella has been a success story in the EU food safety system in the last 10 years. Recent S. Enteritidis outbreaks contributed to a change in this trend in humans and poultry. Further investigations by competent authorities in the field of public health and food safety will be crucial to understand the reasons behind the increase.” 

There were 94 530 human cases of salmonellosis reported in the EU in 2016. S. Enteritidis – the most widespread type of Salmonella, accounted for 59% of all salmonellosis cases originating in the EU and is mostly associated with the consumption of eggs, egg products and poultry meat. 

Campylobacter and Listeria

Campylobacter, the most reported food-borne pathogen in humans, was detected in 246 307 people, an increase of 6.1% compared with 2015. Despite the high number of cases, fatalities were low (0.03%). Levels of Campylobacter are high in chicken meat.

Listeria infections, which are generally more severe, led to hospitalisation in 97% of reported cases. In 2016, listeriosis continued to rise, with 2 536 cases (a 9.3% increase) and 247 deaths reported. Most deaths occur in people aged over 64 (fatality rate of 18.9%). People over 84 are particularly at risk (fatality rate of 26.1%). Listeria seldom exceeded legal safety limits in ready-to-eat foods.

Salmonella food-borne outbreaks increasing 

The 4 786 food-borne disease outbreaks reported in 2016 represent a slight increase in comparison with 2015 (4 362 outbreaks), but the figure is similar to the average number of outbreaks in the EU during 2010–2016. 

Outbreaks due to Salmonella are on the rise, with S. Enteritidis causing one in six food-borne disease outbreaks in 2016. Salmonella bacteria were the most common cause of food-borne outbreaks (22.3%), an increase of 11.5% compared to 2015. They caused the highest burden in terms of numbers of hospitalisations (1,766; 45.6% of all hospitalised cases) and of deaths (10; 50% of all deaths among outbreak cases).

Salmonella in eggs caused the highest number of outbreak cases (1 882).

Australia still has an egg problem: Over 200 with Salmonella across NSW as temps rise

Providing food safety advice without preaching is tricky.

Matching the advice with what happens in reality is damn hard.

Amy, Sorenne and I are hanging out in Canberra – Australia’s capital — for the next couple of days while Amy goes to a French conference and Sorenne teaches me how to play Minecraft.

Dinner last night, including chicken wings and potato-somethings, were both served with aioli.

I asked the server, how was the aioli prepared, is it a commercial product or is it made with raw eggs?

Oh, we make our own aioli. We would never buy the commercial product.

No thanks.

Amy said, serve it on the side, I’ll take the risk.

So did Sorenne, although we did have a chat about microbiology (seize those learning moments).

This in context of health authorities warning people to take precautions to prevent salmonella poisonings, with 201 cases already reported in late November as temperatures start to climb.

Of the 4.1 million cases of food poisoning in Australia each year around a third of reported outbreaks are linked to raw or lightly cooked eggs.

Dr Vicky Sheppeard, Directors of Communicable Diseases at NSW Health said the best defence against salmonellosis was careful food preparation and food storage.

“Products containing undercooked eggs, and the spread of germs in the kitchen, are the most common source of salmonellosis outbreaks in NSW.”

NSW Food Authority CEO Dr Lisa Szabo said using commercially produced products instead of handmade mayonnaise and sauces when preparing food also reduced the risk of Salmonella poisoning.

“It is also much safer to use commercially pasteurised eggs rather than raw eggs in ready-to-eat products such as desserts and dressings,” DrSzabo said.

Good luck with that.

 

3 sick, 1 dead from Salmonella in Tahiti

Three cases of salmonellosis are officially confirmed, in Taravao, in addition to the suspect case of a fourth person who died after having shown the symptoms of salmonella poisoning. 

In a statement released Thursday morning, the Ministry of Health said “three cases of salmonellosis confirmed and a suspected case, occurred in Taravao. “These infections were reported to the Bureau de veille sanitaire between 20 and 28 November. Above all, “one person has died,” says this information, while indicating that ” the main cause of death remains uncertain.”

This person died in the night of November 18 to 19, a few hours after eating an egg dish (Kai Fan). His wife suffered a salmonella infection following this meal. One of two other confirmed cases of salmonellosis also consumed a Kai Fan. These takeaway meals were all purchased in the same Taravao business.

Australia: still has an egg problem: 17 major salmonella outbreaks for Adelaide in 2016/17 linked to pork and eggs

The almost southern most state of Australia, South Australia has a population of 1.7 million people, and yet almost 1,200 South Australians were stricken by food poisoning in the past 12-months.

Katrina Stokes of The Advertiser writes that according to the 2016/17 Health Department report, 17 food poisoning investigations conducted by officials revealed that dairy, poultry and meat products were responsible for the salmonella outbreaks.

New figures from SA Health reveal there have been a total of 1182 salmonella cases so far this year, compared to a total of 1561 in 2016.

Alarmingly, of this year’s cases, 17 per cent have been in children aged five or younger.

The biggest outbreak was at the InterContinental Hotel on July 31 last year after guests ate the buffet breakfast — and the cause was linked to cross contamination from eggs.

Of 140 people who reported feeling unwell, 85 were confirmed cases of salmonella and 20 were admitted to hospital.

Patients were treated for vomiting, diarrhoea, fever and headaches.

Other food poisoning cases in 2016/17 included:

CHILDREN at an out-of-hours care facility were struck down with gastroenteritis and an investigation identified one source was inadequate sanitation procedures in the kitchen. Some of the children also reported consuming eggs in an uncooked cupcake mixture. A total of 24 children were sick and 12 cases confirmed.

WEDDING guests fell ill after eating food, including chicken liver parfait and chicken galantine, at a restaurant. One food poisoning case was confirmed and a total of 12 people were sick.

DODGY egg sandwiches and wraps from a bakery caused a total of eight people to get sick. The source was the egg supplier.

Earlier this year, at least 14 people got sick after eating pork pies from the Pork Pie Shop at Victor Harbor.

An inspection of the bakery identified problems including possible contamination from raw egg wash used on the pies, inadequate storage temperature and cleaning of sanitising of equipment.

A total of 33 people got sick from a rare form of salmonella after eating rockmelon from an interstate producer in July 2016.

SA Health director of food and controlled drugs Dr Fay Jenkins said the exact cause of salmonella was often hard to pinpoint — but eggs, and egg handling, were often the culprit.

“To reduce the risk of sickness, do not use eggs if they are cracked or dirty, wash your hands after handling eggs and keep raw egg products like aioli, mayonnaise and mousse refrigerated,” she said.

How about, cook eggs.

A table of Australian egg outbreaks is available at http://barfblog.com/wp-content/uploads/2017/05/raw-egg-related-outbreaks-australia-5-1-17.xlsx.

Eggs are going to have Salmonella in ways we can’t predict, because we are mere mortals: Brits say, we know better

On the same day that Australia celebrated national egg day with vid-clips of schoolchildren pronouncing their love of eggs, the UK Food Standards Authority says it’s OK for pregnant women to eat raw eggs.

These are both so wrong on so many levels.

The UK’s contribution to international cuisine has been mushy peas and mad cow disease.

The UK Food Standards Authority’s contribution to food policy has been cook your food until it is piping hot, and now, it’s OK for pregnant women to eat raw eggs.

With five daughters, I’ve spent a lot of time around pregnant women, they may feel like Rocky Balboa, but biology don’t work that way.

The Food Standards Agency has announced a change to its advice about eating eggs – infants, children, pregnant women and elderly people can now safely eat raw or lightly cooked eggs that are produced under the British Lion Code of Practice.

The revised advice, based on the latest scientific evidence, means that people vulnerable to infection or who are likely to suffer serious symptoms from food poisoning (such as infants, children, pregnant women and elderly people) can now safely eat raw or lightly cooked hen eggs or foods containing them.

We had previously advised that vulnerable groups should not consume raw or lightly cooked eggs, because eggs may contain salmonella bacteria which can cause serious illness.  

The decision to change the advice is a result of the findings from an expert group that was set up by the Advisory Committee on the Microbiological Safety of Food (ACMSF) in February 2015 to look at egg safety. Its report, published in July 2016, highlighted that the presence of salmonella in UK eggs has been dramatically reduced in recent years, and the risks are very low for eggs which have been produced according to food safety controls applied by the British Lion Code of Practice. More than 90% of UK eggs are produced under this scheme.

Heather Hancock, Chairman of the Food Standards Agency, said: “It’s good news that now even vulnerable groups can safely eat UK eggs without needing to hardboil them, so long as they bear the British Lion mark. The FSA has thoroughly reviewed the scientific evidence about the safety of these eggs, and we’re confident that we can now change our advice to consumers.

“The major reduction in the risk of salmonella in Lion eggs is testament to the work carried out by egg producers. The measures they’ve taken, from vaccination of hens through to improving hygiene on farms and better transportation, have dramatically reduced salmonella levels in UK hens.”

A range of interventions have been put in place across the food chain as part of the Lion scheme including: vaccinating hens, enhanced testing for salmonella, improved farm hygiene, effective rodent control, independent auditing and traceability, and keeping the eggs cool while transporting them from farm to shop.

Great. Show us mere mortals the numbers.

And any science-based body that recommends cooking food until it is piping hot is seriously suspect.

Egg farmer David Brass says the introduction of the British Lion standard has made all the difference.

“We know from back in the ’80s when all the scare started, there was an issue with eggs.

“But what the Lion standard does, it is a fully independent, audited code of practice to make sure we have standards on the farm that make sure we can’t have any of those disease problems again.

“And it has shown time after time, in those intervening years, that it is just a brilliant food safety code.”

Yup, audits make the difference (not).

This won’t end well.

In Australia, the morning shows were filled with fluff about the greatness of eggs, with no mention of the following outbreaks involving raw eggs or raw-egg sauces.

A table of Australian egg outbreaks is available at http://barfblog.com/wp-content/uploads/2015/10/raw-egg-related-outbreaks-australia-10-9-15.xlsx

11M eggs destroyed: Health types in Israel warn of Salmonella threat

Baltimore Jewish Life, one of my must-reads in the tub, reports the Israeli Health Ministry has called on the general public not to buy “Yesh Maohf” eggs with a ‘last date of sale’ of 20 October. Officials are also calling on the tzibur at large to destroy 11 million eggs.

 Officials do not want the eggs returned, for this will spread the infection. Consumers are instructed to take the loss and destroy eggs.

The Ministries of Health and Agriculture emphasize that it is forbidden to consume eggs that have already been purchased and that they must be destroyed by throwing them into the garbage can.

ProMed followed up on this, and was provided with a report from Israeli health types:

The Israeli Ministry of Health is investigating a recent increase in laboratory notifications of _Salmonella enterica_ serovar Enteritidis infections. During May-July 2017 at least 848 patients infected with _S._ Enteritidis were reported, compared with 294 cases in the same period in 2016 (2.9-fold increase). During this period _S._ Enteritidis accounted for 58 percent of salmonellosis cases in Israel which marks a major increase in this serovar. Salmonellosis cases were reported nationwide, with case clusters reported mainly from the Jerusalem and the Southern districts. About 2 percent of cases involved invasive infection.

Several outbreak clusters were reported and investigated during this period in kindergartens, hostels, and restaurants across the country. Epidemiology, trace back, and laboratory data have linked several of the outbreak clusters to eggs with hen farms and egg distributors identified as possible sources. PFGE [pulsed-field gel electrophoresis] analysis of isolates from most reported clusters revealed a shared pulsotype. Further analysis by whole genome sequencing and whole genome MLST (wgMLST) [whole genome multi locus sequence typing] identified several sub-clones. Of particular interest is the identification of a clone from geographically distinct salmonellosis clusters that were temporally linked with a common egg distributor (“Yesh Maof”). This clone has also been detected in the context of a kindergarten outbreak in Southern Israel in 2016. Notably, several disease clusters are associated with _S._ Enteritidis strains belonging to the same pulsotype but accounting for distantly related WGS-types [whole-genome-sequencing types]. Laboratory investigation is still ongoing. It is noteworthy that there have not been any reports of _S._ Enteritidis in any foodstuffs routinely inspected for _Salmonella_ in Israel during the respective period.

An outbreak control team has been set up by the Ministry of Health and Ministry of Agriculture. Joint trace back and trace forward investigations are being carried out in order to identify the source of infection. The Ministry of Agriculture has recently inaugurated a monitoring program for _S._ Enteritidis control in laying hen farms.

In the context of this investigation, enhanced environmental sampling of traced laying hen flocks and farms is being carried out. These activities have led to the detection of _S._ Enteritidis in flocks supplying the above-mentioned distributor and a subsequent egg recall and planned culling of implicated flocks. Additional public health actions include continued risk management and source control in farms or flocks that will be implicated in human infection and/or found to be contaminated, enhanced epidemiological investigations for salmonellosis cases or case clusters of gastrointestinal infection, intensified inspections by the National Food Service and risk communication to the public, with emphasis on the safe handling and consumption of eggs and egg-containing foods.

 

Whole genome sequencing PR in Australia

In a press release story that oozes with promotional fanfare, foodborne illnesses caused by bugs such as salmonella could be cut by a third in NSW within five years, with food and health authorities adding a “revolutionary” tool to their arsenal.

NSW Health and NSW Food Authority have started using whole genome sequencing technology to more quickly identify a foodborne outbreak and connect it with its source, which could reduce illnesses and even deaths.

“[It’s] a significant breakthrough that could help revolutionise how food-borne illnesses are identified, understood, tracked and managed,” said Dr Craig Shadbolt, the Food Authority’s acting chief executive.

“This will be invaluable in terms of achieving the NSW Government’s Food Safety Strategy goal of reducing foodborne illnesses caused by salmonella, campylobacter and listeria by 30 per cent by 2021.”

That sounds nice, but some practical steps, like not using raw eggs in mayo, aoili, or baked Chinese ice cream, would go farther. In Australia, rates of foodborne salmonella poisoning have climbed from 38 per 100,000 people in 2004 to 76 per 100,000 in 2016, with a record-breaking 18,170 cases last year, according to the National Notifiable Diseases Surveillance System.

A table of raw-egg-based outbreaks in Australia is available at: http://barfblog.com/wp-content/uploads/2017/05/raw-egg-related-outbreaks-australia-5-1-17.xlsx-