Be serious about B. cereus

Employing advanced genetic-tracing techniques and sharing the data produced in real time could limit the spread of bacteria – Bacillus cereus – which causes foodborne illness, according to researchers. As part of a recent study, researchers at Penn State University implemented whole-genome sequencing of a pathogen-outbreak investigation, following an outbreak of foodborne illnesses in New York in 2016.

“Here, in our study, we use this approach for the first time on Bacillus cereus,” says Jasna Kovac, assistant professor of Food Science at Penn State. “We hope that whole-genome sequencing of Bacillus will be done more often as a result of our research, as it allows us to differentiate between the various species of Bacillus cereus group and project the food-safety risk associated with them.”

The project marks the first time researchers have conducted whole-genome sequencing to investigate a Bacillus cereus outbreak to link isolates from human clinical cases to food. The New York outbreak in 2016 lasted less than a month and stemmed from contaminated refried beans served by a small Mexican restaurant chain.

Although the toxin-producing bacteria are estimated to cause 63,400 foodborne disease cases per year in the US, Bacillus cereus does not receive the attention given to more deadly foodborne pathogens such as Listeria and Salmonella.

Because illness caused by Bacillus cereus typically resolves within days and outbreaks are self-limiting in nature, foodborne illness caused by members of this pathogen group are often under-reported. Although there have been reports of severe infections resulting in sudden patient death, Bacillus cereus group isolates linked to human clinical cases of foodborne disease typically do not undergo whole-genome sequencing, as is becoming the norm for other foodborne pathogens.

In this case, the New York State Department of Health coordinated the epidemiological investigations. The methods included a cohort study, food-preparation review, a food-product traceback, testing of the environment, food and water and an inquiry at a production plant in Pennsylvania that produced the contaminated refried beans. The researchers sequenced the majority of Bacillus cereus isolates, from both food and humans, at the Penn State Genomic Core Facility, which is part of the Huck Institutes of the Life Sciences.

She’s no Churchill: ‘Scrape the mould off’ Theresa May’s unusual advice horrifies Brits

Microganisms are only visible when they are numerous.

I would throw away the entire jam to get rid of the unseen bugs, which number in the trillions.

Theresa May, chief Brexit strategist, PM and armchair microbiologist, shocked the UK by telling a Cabinet meeting Tuesday that she “will not throw away a jar of jam if it has gone mouldy on top”  according to the Daily Mail,

Instead, the newspaper reported, “she scrapes off the mould and eats the good preserve left underneath”.

May considered the rest of the jam to be “perfectly edible”, a Whitehall source told the Mail, and instead of binning food past its best-before date shoppers should “use common sense” to check if it’s edible.

The tip came during a Cabinet discussion on how to reduce food waste.

Social media immediately set about debating on whether this was good food advice, but more importantly, whether it was a metaphor for Brexit.

Nick Miller of The Canberra Times writes, some asked if Brexit was a case of “jam tomorrow.”

As the country lurches towards a potential no-deal Brexit, featuring potential food and medicine shortages, there has been a new focus on making the most of indigenous food supplies.

The UK is Europe’s biggest producer of citrus jams and marmalades, however France is by far the biggest producer of other types of jams and purees, followed by Germany.

If there are significant customs delays then breakfasts across the UK could be disrupted.

It may also be significant that the British government has been simulating the immense traffic jams expected to materialise around its southern ports if there is a no-deal Brexit.

Interestingly, the British government revealed in 2016 that its post-Brexit ‘Food and Drink International Action Plan’ would include a major campaign to sell British jam to Australia.

Asked on Wednesday if May thought people should follow her example, the Prime Minister’s spokesman said it was a “matter for the individual”.

Time magazine reported in 2015 that “when visible mould is present, its tentacles – called ‘threads’ – have likely penetrated deep into your food [unless it’s a hard cheese], contaminating even those parts that appear to be mould-free”.

They added that mould exposure can produce mycotoxins leading to respiratory problems, allergic reactions and even cancer.

However, in 2014, a “mould expert” told the BBC that “the moulds you find on jam are fine – just scrape them off”.

Rotavirus or Norovirus: They’re both spread by poo and lousy handwashing

Rotavirus is a leading cause of acute gastroenteritis (AGE) in children and is highly transmissible. In this study, we assessed the presence of AGE in household contacts (HHCs) of pediatric patients with laboratory-confirmed rotavirus.

 

Between December 2011 and June 2016, children aged 14 days to 11 years with AGE were enrolled at 1 of 7 hospitals or emergency departments as part of the New Vaccine Surveillance Network. Parental interviews, medical and vaccination records, and stool specimens were collected at enrollment. Stool was tested for rotavirus by an enzyme immunoassay and confirmed by real-time or conventional reverse transcription-polymerase chain reaction assay or repeated enzyme immunoassay. Follow-up telephone interviews were conducted to assess AGE in HHCs the week after the enrolled child’s illness. A mixed-effects multivariate model was used to calculate odds ratios.

Overall, 829 rotavirus-positive subjects and 8858 rotavirus-negative subjects were enrolled. Households of rotavirus-positive subjects were more likely to report AGE illness in ≥1 HHC than were rotavirus-negative households (35% vs 20%, respectively; P < .0001). A total of 466 (16%) HHCs of rotavirus-positive subjects reported AGE illness. Of the 466 ill HHCs, 107 (23%) sought healthcare; 6 (6%) of these encounters resulted in hospitalization. HHCs who were <5 years old (odds ratio, 2.2 [P = .004]) were more likely to report AGE illness than those in other age groups. In addition, 144 households reported out-of-pocket expenses (median, $20; range, $2–$640) necessary to care for an ill HHC.

Rotavirus-associated AGE in children can lead to significant disease burden in HHCs, especially in children aged <5 years. Prevention of pediatric rotavirus illness, notably through vaccination, can prevent additional illnesses in HHCs.

Evidence for household transmission of rotavirus in the United States, 2011-2016

7.feb.19

Journal of the Pediatric Infectious Diseases Society, https://doi.org/10.1093/jpids/piz004

Mary E Wikswo, Umesh D Parashar, Benjamin Lopman, et al

https://academic.oup.com/jpids/advance-article-abstract/doi/10.1093/jpids/piz004/5310348?redirectedFrom=fulltext

Raw is risky: Drug-resistant brucellosis linked to raw milk

The U.S. Centers for Disease Control and Prevention and state health officials are investigating potential exposures to Brucella strain RB51 (RB51) in 19 states, connected to consuming raw (unpasteurized) milk from Miller’s Biodiversity Farm in Quarryville, Pennsylvania. One case of RB51 infection (brucellosis) has been confirmed in New York, and an unknown number of people may have been exposed to RB51 from drinking the milk from this farm. This type of Brucella is resistant to first-line drugs and can be difficult to diagnose because of limited testing options and the fact that early brucellosis symptoms are similar to those of more common illnesses like flu.­

The New York case is the third known instance of an infection with RB51 associated with consuming raw milk or raw milk products produced in the United States. The other two human cases occurred in October 2017 in New Jersey and in August 2017 in Texas. Those cases reported drinking raw milk from an online retailer and a Texas farm, respectively. In addition to these three confirmed cases, hundreds of others were potentially exposed to RB51 during these three incidents.

RB51 is a live, weakened strain used in a vaccine to protect cows against a more severe form of Brucella infection that can cause abortions in cows and severe illness in people. On rare occasions, cows vaccinated with RB51 vaccine can shed the bacteria in their milk. People who drink raw milk from cows that are shedding RB51 can develop brucellosis.

People who consumed raw milk or raw milk products from this dairy farm since January 2016 may have been exposed and should talk to their doctor.

People who are still within six months of the date they last consumed the raw milk are at an increased risk for brucellosis and should receive antibiotics to prevent an infection and symptoms, and should monitor their health for possible symptoms for six months. If symptoms develop, they should see their doctor immediately for testing.

Milk samples from Miller’s Biodiversity tested positive for RB51. A cow that tested positive for RB51 has been removed from the milking herd.

Fun with fermentations: Black coffee in bed with help from microbes

Australia is, for reasons I’ll never understand, a country of coffee snobs, with their baristas and their 20-minute preparation times and the $4.50 a cup.

No Tim Hortons here (sadly, the co-founder of the venerable Canadian chain passed away today).

According to research published February 1 in the journal, Applied and Environmental Microbiology, when processing coffee beans, longer fermentation times can result in better taste, contrary to conventional wisdom. Lactic acid bacteria play an important, positive role in this process. Other species of microbes may play a role in this process as well, but more research is needed to better understand their role.

“A cup of coffee is the final product of a complex chain of operations: farming, post-harvest processing, roasting, and brewing,” said principal investigator Luc De Vuyst, M.Sc., Ph.D., Professor of Industrial Microbiology and Food Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium. “There are several variants of post-harvest processing, among which wet processing and dry processing are the most common.” Wet processing—commonly used for Arabica and specialty coffees—is the step that includes fermentation.

“We carried out the research at an experimental farm in Ecuador through a multiphasic approach, encompassing microbiological, metabolomics, and sensory analysis,” said Dr. De Vuyst.

Fermentation was of particular importance. During extended fermentation, leuconostocs—a genus of lactic acid bacteria used in the fermentation of cabbage to sauerkraut and in sourdough starters—declined in favor of lactobacilli, said Dr. De Vuyst. Lactic acid bacteria were already present before fermentation, and these acid tolerant lactobacilli proliferated even more during this process.

However, it is challenging to draw a causal link between the microbiota and the volatile compounds in the beans—those compounds that contribute to the coffee’s smell – since many of these compounds can be of microbial, endogenous bean metabolism, or chemical origin,” said Dr. De Vuyst.

“However, we did see an impact of the microbial communities, in particular the lactic acid bacteria,” said Dr. De Vuyst. They yielded fruity notes, and may have “had a protective effect toward coffee quality during fermentation because of their acidification of the fermenting mass, providing a stable microbial environment and hence preventing growth of undesirable microorganisms that often lead to off-flavors,” he said.
“Furthermore, there is a build-up of the fermentation-related metabolites onto the coffee beans, which affects the quality of the green coffee beans and hence the sensory quality of the coffees brewed therefrom,” said Dr. De Vuyst.

Dr. De Vuyst emphasized that how each stage of processing influences the taste of coffee remains mostly uncharted. “We were aware of many different microorganisms during wet coffee fermentation — enterobacteria, lactic acid bacteria, yeasts, acetic acid bacteria, bacilli, and filamentous fungi,” said Dr. De Vuyst, but it is still unknown how most bacteria influence this process.

The work was a collaboration between the Vrije Universiteit Brussel, and Nestlé Research. “Nestlé was interested in the fundamental aspects of coffee processing, in particular, the post-harvest processing chain, in order to correlate it with the roasting process and of course the final cup quality,” said Dr. De Vuyst.

Indonesian earthquake victims suffer food poisoning at shelter

I have been known to tell my partner, your attempts at help are futile, please stay away.

Ruslan Sangadji of The Jakarta Post reports that dozens of people from Kabonena and Tipo subdistricts in Palu, Central Sulawesi, who were displaced by a recent earthquake, have been hospitalized for reported food poisoning after consuming donated food on Saturday.

Badrun, one of the food poisoning victims, said the food was distributed to the shelter at around 11 a.m. local time. The displaced people did not feel anything strange as they ate the food but an hour later they started to feel dizzy and nauseous, he said.

The victims – mostly children – were rushed to Anutapura Palu Hospital.

Anutapura Palu Hospital deputy director for medical services Herry Mulyadi said his office had recorded that at least 38 people had been admitted to the hospital, while others were taken to other hospitals.

“Every single one of them complained about feeling dizzy and nauseous,” Herry said.

By Sunday, more than half of the food poisoning victims had been discharged.

Central Sulawesi Governor Longki Djanggola, who visited the victims at the hospital on Saturday evening, said that everyone should ensure that the food and drinks they donated were safe for consumption.

“I thank everyone who took part in helping the displaced people through their donations; but people, at the same time, have to remain vigilant before consuming [the food],” he said.

Samples of the food had been taken to Central Palu’s medical laboratory for examination, Longki said.

It remains unclear who sent the food to the shelter.

90 soldiers contracted Q fever while serving in Afghanistan

At least 90 British military personnel have been diagnosed with confirmed cases of Q fever after serving in Helmand, Afghanistan, a British court heard this week.

According to a UK military news outlet, Forces Network, a consultant in infectious diseases and tropical medicine told the Central London Country Court on Tuesday that 90 confirmed cases of Q Fever had been recorded among British soldiers who had served in Helmand.

Lieutenant Colonel Mark Bailey’s testimony was heard in the case of Wayne Bass, a private with 2nd Battalion the Mercian Regiment, who said his life has been ruined after he contracted the disease while in Helmand in 2011/2012.

Humans can catch Q fever by breathing in dust from the feces of infected farm animals such as sheep, cattle and goats.

During his tour, his lawyers said Bass was in contact with goats and sheep and “was often required to take cover and jump through ditches and crawl along the ground – coming into contact with animal products and excrement”.

Bass, 34, was medically discharged from the Army in 2014 because of his Q fever and chronic fatigue symptoms.

Bailey, who specializes in infectious diseases and tropical medicine, and a national expert in Q fever, gave evidence during the second day of the trial.

Under questioning from Theo Huckle QC for Bass, Bailey said he has 90 military and 10 civilian cases in his care after they were referred to him.

He confirmed the 90 had served in Helmand and said the number of military cases “built up from 2008”, Forces Network reported.

Bailey told the court: “We have seen no new cases since 2014 from Afghanistan. Occasionally we get other military cases from other locations. Cyprus most recently.”

Bailey said he had seen “one British soldier who very, very nearly died” as a result of Q fever and subsequent complications, but there have been no UK deaths in his group.

In court documents setting out the case, it is argued that the MoD should have considered using Doxycycline, an antibiotic used to treat Q fever, as an anti-malarial drug, Forces Network reported.

The MoD however denies failing in its duty of care – pointing out that a vaccine used by some countries is not licensed in the UK.

Student dies after eating five-day old pasta that had been left out

(Correction: This actually happened in 2008 and the paper was published in 2011. Still a good reminder of the importance of temperature control.)

Who doesn’t experiment in college?

But meddling with microbiology can be particularly risky.

A student died after eating leftover pasta that had been left on his kitchen benchtop for five days.

The 20-year-old from the Brussels in Belgium became sick after eating leftover spaghetti with tomato sauce which had been prepared five days earlier and stored at room temperature.

After becoming violently ill, he went to bed to try and sleep the sickness off, only to be found dead in bed the next morning by his devastated parents.

An autopsy later revealed he died from Bacillus cereus.

The story has been featured by Dr Bernard, a licenced practitioner who studies and shares bizarre medical cases from around the world on his YouTube channel.

Dr Bernard analysed the case, which originally featured in the US Journal of Clinical Microbiology, along with several others in a dramatised re-enactment, explaining the harmful bacteria caused AJ’s liver to shut down.

Samples of spoiled pasta and tomato sauce samples were also analysed, with the National Reference Laboratory for Food-borne Outbreak confirming the spaghetti was contaminated with “significant amounts” of the B. cereus — while it was absent in the sauce.

Pasteurization works: Acai fruit can transmit Chagas disease

I need to start playing the banjo again.

Artisan juice made with açaí, the fruit of a palm that grows in the rainforests of northern Brazil, could be a major source of infection with Trypanosoma cruzi, the parasite that causes Chagas disease, two studies suggest.

The disease affects around eight million people worldwide, according to the World Health Organization (WHO), and is transmitted by triatomine bugs ‒ blood-sucking insects known by several different names in Latin America (chinche, chirimacha and barbero, among others).
Symptoms of the disease can appear in the first months after the infection, but most people do not show signs of the disease, which makes early diagnosis difficult. When the disease evolves to the chronic phase it can cause cardiac and digestive complications.

The new studies suggest that people can become infected by consuming açaí when the insect vector, or its faeces, are accidentally mixed with the fruit while blending the juice.

The fruit comes into contact with the vector during processing and storage: while kept in open baskets, the açaí fruit ferments and generates carbon dioxide, which attracts the triatomine insect.

One of the papers, published this month in Emerging Infectious Diseases, studied ten individuals in the cities of Manaus and Labrea, in the Brazilian state of Amazonas, who had symptoms of fever, headaches and general weakness. The researchers found that these patients were infected with the same varieties of parasite found in artisan açaí juice they had consumed days earlier.

“The findings reinforce the hypothesis that in the Amazon region, açaí juice prepared by hand is one of the sources of infection by the parasite,” says Marcus Lacerda, a physician at the Tropical Medicine Foundation in Manaus, and one of the authors of the study.

Another study, published in the magazine Memórias do Instituto Oswaldo Cruz, confirms that the growth of Chagas disease in Pará, one of the country’s highest açaí juice-consuming states, is associated with the harvest season of the fruit between August and December.

This conclusion was based on analysis of the state records from Brazil’s Information System for Notifiable Diseases (SINAN), between 2000 and 2016. During this period, 16,807 cases of Chagas disease were reported, and 2,030 of them were confirmed. Most of the confirmed cases occurred during the second half of each year.

Juliana de Meis, immunologist of the Oswaldo Cruz Institute (IOC-Fiocruz), in Rio de Janeiro, tells SciDev.Net that further analysis of the data suggests that oral transmission increased much more than other infection routes in that period. De Meis believes that this new study adds to evidence that açaí is one of the main sources of infection by T. cruzi in the region.

According to the Brazilian Institute of Geography and Statistics, 54 per cent of the national production (800,000 tons of açaí per year) comes from 13,000 producers in the state of Pará.

In Belém, the capital of Pará, it is estimated that 200,000 liters of açaí are consumed per day during harvest season ‒ double the quantity consumed in other seasons. This makes it the second most consumed food in the city during that season.

Part of the local production is exported to other regions of Brazil, and further afield to the United States and European countries.

Chagas disease is one of the major health problems facing countries and states in the Amazon region, causing disability in infected people and more than 10,000 deaths per year.

Cases of the disease are growing systematically, says the second study, specifically in Brazil’s Northern Region. According to the 2015 epidemiological bulletin of the country’s Ministry of Health, 812 cases of oral transmission of Chagas disease were confirmed in the state of Pará between 2000 and 2013.

“However, everything indicates that these numbers are an underestimate”, points out De Meisor Angela Junqueira, a biologist at the Laboratory of Parasitic Diseases of IOC-Fiocruz, açaí juice contamination can be avoided by appropriate handling of the fruit, including dipping the fruit in boiling water for ten seconds and then spraying them with cold water.

“Although this procedure has been mandatory since 2012, the practice has not been used in the region”, she tells SciDev.Net. 

Junqueira says the risks of disease transmission through açaí consumption outside of the northern region are low, because juice exported to other regions or countries undergo mandatory pasteurization.

“In the Northern Region … it is essential to invest in training of physicians and microscopy specialists so that they can identify the symptoms and make early lab diagnosis”, she suggests.

“It is also necessary to focus on staff training so that they adopt good management practices during the processing of açaí, such as covering the baskets and blenders, and washing the fruit with boiling water”, says Junqueira, adding that the fruit is important for the local economy and diet.

A book that will make you terrified of your own house

That’s the headline in the N.Y. Times, but as I try to tell my 10-year-old (seen here with one of her older sisters as a 4-years-old after the skating coach told her she had to wear figure skates and not hockey skates, and I said, I’m Canadian, your wrong, and when was the last time Russian women successfully competed in ice hockey) there are microbes all around us, we just have to try and understand them.

I’m still convinced we are all hosts on a viral planet.

And I figure Schaffner should review this book, but he’s a busy dude, so I’ll do it.

From Microbes to Millipedes, Camel Crickets, and Honeybees, the Natural History of Where We Live by Rob Dunn is a collection of the myriad microbial life-forms that take up residence in a typical American showerhead, I’m starting to think maybe that young man was onto something.

With an army of collaborators, Dunn, a professor of applied ecology at North Carolina State University, took samples of the gunk inside hundreds of showerheads, and found a profusion of microbial fauna. Tap water itself, he writes in the chatty, informative “Never Home Alone,” teems with amoebas, bacteria, nematodes and crustaceans. As the water passes through the showerhead, these microbes lay down a kind of scaffolding known as biofilm to protect themselves from getting washed away with every ablution. They make the biofilm “out of their own excretions,” Dunn writes bluntly. “In essence, by working together, the bacteria poop a little indestructible condominium in your pipes.”

It gets worse. Filtered through that poop-biofilm, the water that washes over you, as you supposedly scrub yourself clean, might contain not only all those harmless amoebas and nematodes but a few bacteria that can be dangerous — in particular some species of Mycobacterium, cousins of the Mycobacterium that causes tuberculosis. And the pathogens are there because we provided the perfect breeding ground for them, when we tried to purify our tap water in the first place. Municipal water treatment plants use chlorine and other chemicals that kill off the bacterium’s natural predators, allowing Mycobacterium to thrive. Tap water that comes from a well, in contrast, has never gone through a treatment plant and has a rich microbial life. It might look more dangerous, but it’s actually safer, Dunn explains. All those organisms in well water are themselves harmless, and they tend to fight off the potentially dangerous ones like Mycobacterium — that’s how biodiversity works.

News from the showerhead biome is just one part of this fact-filled, occasionally disgusting, slightly alarming book. Dunn has been involved in an obsessive quest to document the tiny inhabitants of indoor environments, a project that involves teams of professional and amateur bug-watchers to take samples not only from showerheads but from door frames, refrigerators, hot water heaters, cellars, toilets, pillowcases, all sorts of surfaces from the places we call home. These workers swab and seal, swab and seal, and send their thousands of samples to Dunn’s lab in Raleigh, or to his other lab at the Natural History Museum of Denmark, for an ongoing microbial census.