Genetics is cool: Scientists find single letter of genetic code that makes African Salmonella so dangerous

Scientists at the University of Liverpool have identified a single genetic change in Salmonella that is playing a key role in the devastating epidemic of bloodstream infections currently killing around 400,000 people each year in sub-Saharan Africa.

Invasive non-typhoidal Salmonellosis (iNTS) occurs when Salmonella bacteria, which normally cause gastrointestinal illness, enter the bloodstream and spread through the human body. The African iNTS epidemic is caused by a variant of Salmonella Typhimurium (ST313) that is resistant to antibiotics and generally affects individuals with immune systems weakened by malaria or HIV.

In a new study published in PNAS, a team of researchers led by Professor Jay Hinton at the University of Liverpool have identified a specific genetic change, or single-nucleotide polymorphism (SNP), that helps the African Salmonella to survive in the human bloodstream.

Professor Hinton explained: “Pinpointing this single letter of DNA is an exciting breakthrough in our understanding of why African Salmonella causes such a devastating disease, and helps to explain how this dangerous type of Salmonella evolved.”

SNPs represent a change of just one letter in the DNA sequence and there are thousands of SNP differences between different types of Salmonella. Until now, it has been hard to link an individual SNP to the ability of bacteria to cause disease.

Using a type of RNA analysis called transcriptomics, the scientists identified SNPs that affected the level of expression of important Salmonella genes. After studying 1000 different SNPs, they found a single nucleotide difference that is unique to the African ST313 strain and causes high expression of a virulence factor called PgtE that prevents Salmonella being killed in the bloodstream.

The scientists then used an advanced genetic technique to switch the SNP found in the African strain to the version found in the type of Salmonella that causes food poisoning and gastroenteritis globally. Finally, they used an animal infection model to show that the bacteria with the altered SNP had lost their ability to cause disease.

Professor Hinton added: “We’ve developed a new investigative approach to understand bacterial infection, which is the culmination of six years of work. This combination of genomics and transcriptomics could bring new insights to other important pathogens, and prepare us for future epidemics.”

Professor Melita Gordon, a University of Liverpool clinician-scientist working in Malawi, who was involved in the project, said: “The ability of iNTS Salmonella strains to cause such serious disease leads to devastating and frequently fatal consequences for very young children, and for adults who may be the chief breadwinners in their homes and communities. We see iNTS disease placing an enormous burden on thinly-stretched local health facilities and hospitals in Malawi, particularly because diagnosis is difficult, and treatment options are limited. It is now urgent that a vaccine is developed to combat this dangerous infection.”

Disa L. Hammarlöf, Carsten Kröger, Siân V. Owen, Rocío Canals, Lizeth Lacharme-Lora, Nicolas Wenner, Anna E. Schager, Timothy J. Wells, Ian R. Henderson, Paul Wigley, Karsten Hokamp, Nicholas A. Feasey, Melita A. Gordon, Jay C. D. Hinton. Role of a single noncoding nucleotide in the evolution of an epidemic African clade ofSalmonella. Proceedings of the National Academy of Sciences, 2018; 201714718 DOI: 10.1073/pnas.1714718115

‘When the going gets weird, the weird turn pro’ To sate China’s appetite, African donkeys are stolen and skinned

An edited version of this fascinating Times story is below:

“This is the spot,” said Morris Njeru, gazing down at a tangled patch of farmland where he recently found the bloody corpses of David, Mukurino and Scratch — his last donkeys.

Mr. Njeru, 44, a market porter who depends on his animals to ferry goods around this city, had already lost five donkeys earlier in the year. In each case, the thieves slit the animals’ throats and skinned them from the neck down, leaving the meat to vultures and hyenas.

Four months later, all Mr. Njeru could find of the animals was a single hoof, which he pocketed as a memento.

Rachel Nuwer of the New York Times writes there are scant remains, too, of Mr. Njeru’s once comfortable life. Without his animals, his income plummeted from nearly $30 per day to less than $5. He can no longer afford payments on a loan for a small piece of property he rented, and he fears he will have to take his child from boarding school.

“My life has completely changed,” he said. “I was depending on these donkeys to feed my family.”

For Mr. Njeru and millions of others around the world, donkeys are the primary means to transport food, water, firewood, goods and people. In China, however, they have another purpose: the production of ejiao, a traditional medicine made from gelatin extracted from boiled donkey hides.

Ejiao was once prescribed primarily to supplement lost blood and balance yin and yang, but today it is sought for a range of ills, from delaying aging and increasing libido to treating side effects of chemotherapy and preventing infertility, miscarriage and menstrual irregularity in women.

While ejiao has been around for centuries, its modern popularity began to grow around 2010, when companies such as Dong-E-E-Jiao — the largest manufacturer in China — launched aggressive advertising campaigns. Fifteen years ago, ejiao sold for $9 per pound in China; now, it fetches around $400 per pound.

As demand increased, China’s donkey population — once the world’s largest — has fallen to fewer than six million from 11 million, and by some estimates possibly to as few as three million. Attempts to replenish the herds have proved challenging: Unlike cows or pigs, donkeys do not lend themselves to intensive breeding. Females produce just one foal per year and are prone to spontaneous abortions under stressful conditions.

So Chinese companies have begun buying donkey skins from developing nations. Out of a global population of 44 million, around 1.8 million donkeys are slaughtered per year to produce ejiao, according to a report published last year by the Donkey Sanctuary, a nonprofit based in the United Kingdom.

“There’s a huge appetite for ejiao in China that shows no signs of diminishing,” said Simon Pope, manager of rapid response and campaigns for the organization. “As a result, donkeys are being Hoovered out of communities that depend on them.”

In November, researchers at the Beijing Forestry University warned that China’s demand for ejiao may cause donkeys “to become the next pangolin.”

“In 2016, this business of donkeys erupted,” said Obassy Nguvillah, a police superintendent in Tanzania’s Monduli district, near the Kenyan border. “There were increasing numbers of cases of guys passing into the Maasai area, taking people’s donkeys and transporting them to the Chinese-owned processing plant.”

In Esilalei — a village located on a sprawling, drought-plagued savanna under Mr. Nguvillah’s watch — residents lost nearly 475 donkeys in a single year. While about 175 of the animals were recovered by tracking the thieves into the bush, police believe the remainder were sold to slaughterhouses. Unable to afford replacements, the former owners are still reeling.

Unlike Tanzania, Kenya’s donkey skin trade shows no signs of slowing. In 2016, prices for skins were fifty times higher than in 2014, while prices for live donkeys have nearly tripled, from about $60 to $165.

The country’s three abattoirs — all of which have Chinese owners or partners — reported processing just under 100,000 donkeys in two years, according to a government memo. Both skin and meat are exported to China, usually through Vietnam or Hong Kong.

Seventeen skin traders have also opened shop, mostly in Nairobi, and a fourth abattoir is rumored to be on the way. The abattoir owners insist that they are bettering the country by generating jobs and paying handsome prices for unneeded donkeys.

“This business has helped so many people,” said John Kariuki, director of Star Brilliant Donkey Export Abattoir in Naivasha. “Instead of having to sell cows and goats, Maasai pastoralists are selling donkeys to pay their children’s school fees.”

Goldox Donkey Slaughterhouse in Baringo County — the largest of Kenya’s abattoirs, claiming to process some 450 donkeys a day — also attempts to spread good will by providing free water to neighbors, and by paying school fees for four local children.

Waste disposal has become a significant issue. Last fall, Goldox began dumping donkey remains at a parcel of land it purchased in Chemogoch village, down the road from its slaughterhouse.

After residents living adjacent to the site complained, the company began burying the waste rather than leaving it in the open. But neighbors say the situation is still unacceptable, accusing the company of contaminating ground water and breeding disease.

 “Should we go into the cocaine business or the sale of elephant tusks just because it makes money?” asked Dr. Onyango

From Promed: E. coli O157 in Africa, 1992

The Epicore Global Surveillance Project reports that in 1992, a large outbreak of bloody diarrhea caused by Escherichia coli O157 infections occurred in southern Africa.

Swaziland-Bucket-BrigadeIn Swaziland, 40,912 physician visits for diarrhea in persons aged 5 years and older were reported during October through November 1992. This was a 7-fold increase over the same period during 1990-91. The attack rate was 42 percent among 778 residents we surveyed. Female gender and consuming beef and untreated water were significant risks for illness.

E. coli O157:NM was recovered from 7 affected foci in Swaziland and South Africa; 27 of 31 patients and environmental isolates had indistinguishable pulsed-field gel electrophoresis patterns. Compared with previous years, a 5-fold increase in cattle deaths occurred in October 1992. The 1st heavy rains fell that same month (36 mm), following 3 months of drought. Droughts, carriage of E. coli O157 by cattle, and heavy rains with contamination of surface water appear to be important factors contributing to this outbreak.

Early in November 1992, physicians arriving for duty at a small hospital on a sugar plantation in Swaziland found over 100 persons sprawled on the ground in front of the casualty department. Many had bloody diarrhea, and almost all were suffering severe abdominal pains. The next day, the number of patients with the dysenteric illness nearly doubled, yet stool specimens sent to local laboratories did not yield common parasitic or bacterial pathogens, including Shigella spp. With the etiologic agent still unknown into the 2nd week of the outbreak, specimens were forwarded to a reference laboratory in South Africa, where a surprising discovery was made: E. coli O157 had emerged in Africa.

An outbreak of E. coli O157 infections was heretofore unheard of in Africa or, for that matter, anywhere in the developing world. E. coli O157 had been isolated only once before in southern Africa, from an elderly man undergoing surgery for lower gastrointestinal bleeding in Johannesburg in 1990. Carriage of E. coli O157 by cattle, cattle deaths secondary to drought, and heavy rains that resulted in contamination of surface water were important factors contributing to the emergence of E. coli O157 in Africa. Given that drought and heavy rains will likely recur in Africa, the possibility that E. coli O157 will once again emerge to cause a major regional outbreak cannot be excluded. Clinicians need to be aware of this so that delayed diagnosis and inappropriate treatment resulting in loss of lives can be avoided.

Basil as a source of foodborne illness

I’ve got a recipe for mango-basil-ginger pork that I’m going to try out for dinner shortly before my hockey game (and to deal with some left-over pork loin).

mango.parisAnd it’s mango season here. Sorenne’s new favorite fruit.

The problem is, basil has been implicated in a number of microbe-associated foodborne illnesses across the world, and the source of contamination has often been traced back to the production and/or processing stages of the supply chain. The aim of this study was to evaluate the microbiological quality of fresh basil from the point of production to the retail outlet in the Gauteng and Northwest Provinces of South Africa.

A total of 463 samples were collected over a 3-month period from two large-scale commercial herb producing and processing companies and three retail outlets. The microbiological quality of the samples was assessed based on the presence or absence of Escherichia coli O157:H7 and Salmonella Typhimurium and the levels of the indicator bacteria E. coli and total coliforms. 

Salmonella Typhimurium was detected on four basil samples (0.9%) arriving at the processing facility and at dispatch, but no E. coli O157:H7 was detected throughout the study. Total coliform counts were 0.4 to 4.1 CFU/g for basil, 1.9 to 3.4 log CFU/ml for water, and 0.2 to 1.7 log CFU/cm2 for contact surfaces, whereas E. coli was detected in the water samples and only once on basil. The Colilert-18 and membrane filter methods were used to analyze water samples, and a comparison of results revealed that the Colilert-18 method was more sensitive.

Strong evidence suggests that high numbers of coliforms do not necessarily indicate the presence of Salmonella Typhimurium. The study results highlight the importance of effective implementation of food safety management systems in the fresh produce industry.

I’m cooking mine.

Microbiological status and food safety compliance of commercial basil production systems

Journal of Food Protection, January 2016, No. 1, pp. 4-178, pp. 43-50(8)

DOI: http://dx.doi.org/10.4315/0362-028X.JFP-15-182

Willeke  de Bruin, Denise Otto, Lise Korsten

http://www.ingentaconnect.com/content/iafp/jfp/2016/00000079/00000001/art00006

Salmonella major killer of young children in Africa

Link

Invasive Salmonella infections in sub-Saharan Africa are a major cause of child illness and deaths, a new body of research into this usually overlooked infectious disease has revealed.

salm.africaIn the West, Salmonella is commonly thought of as a bacterium responsible for relatively benign cases of food poisoning. However, a supplement to the leading infectious diseases journal Clinical Infectious Diseases now exposes the unacceptable toll of sickness and death caused by invasive Salmonella infections in sub-Saharan Africa.

The supplement, sponsored by New Zealand’s University of Otago and supported by a grant from the Bill & Melinda Gates Foundation, is a key output of a project to better understand the disease burden of this major cause of child death in sub-Saharan Africa.

Guest edited by Professor John Crump, Co-Director of the University’s Centre for International Health, and by Professor Robert Heyderman, Professor of Infectious Diseases and International Health, at University College London, the supplement emerged from a consensus meeting of experts held in Malawi last year, supported by the Wellcome Trust and Bill & Melinda Gates Foundation.

The supplement includes 19 scientific papers that describe the toll of invasive Salmonella infections in Burkina Faso, Ethiopia, Gambia, Ghana, Guinea-Bissau, Madagascar, Mali, Nigeria, Kenya, Democratic Republic of Congo, Malawi, Mozambique, Senegal, South Africa, Sudan, and Tanzania.

It also includes papers on the application of genetic fingerprinting and mathematical modeling to understand disease sources and modes of transmission, as well as vaccines and other prevention measures.

“Invasive Salmonella infections include typhoid fever, a disease that is widely appreciated by the public, but also non-typhoidal Salmonella (often abbreviated as NTS) that tends to be thought of as a cause of diarrhoeal disease in the west but in sub-Saharan Africa it is the leading cause of sepsis or blood poisoning,” said Professor Crump.
“NTS occurs in infants and young children, particularly those with malaria and malnutrition, and in HIV-infected adults. About 20 percent of those who get Salmonella blood poisoning will die.”

“The papers in the supplement demonstrate not only that typhoid fever is underappreciated problem in Africa, but also bring to the fore considerable new data to underpin the first-ever global disease burden estimates for invasive NTS disease that were published earlier this year. The estimates were that in 2010, NTS caused 3.4 million illnesses and 681,000 deaths worldwide, with the majority in sub-Saharan Africa,’ said Professor Heyderman.

“This collection of papers support other evidence that invasive Salmonella is a leading cause of severe bacterial disease in Africa, urgently requiring investment in both vaccine and non-vaccine control measures.”

One of the papers from western Kenya shows that the majority of NTS strains are now resistant to most antibiotics available in Africa.

“With options for treatment diminishing, we must renew our efforts to prevent these severe bacterial infections,” said Professor Heyderman.

The data published in this supplement will be available to the scientific community, including groups at the World Health Organization and the Institute for Health Metrics and Evaluation who are responsible for estimating the global burden of diseases.

“These data are key to improving estimates of typhoid fever in Africa and adding invasive non-typhoidal Salmonella disease to the global causes of illness and death. Currently, the number of illnesses and deaths associated with Salmonella diarrhea are counted, but not the number of Salmonella sepsis illnesses and deaths,” said Professor Crump.

In Africa, a deadly salmonella strain takes hold

Salmonella is an infectious agent with many faces, appearing in a multitude of strains affecting animals and humans. A distinct form of the bacterial invader has emerged in sub-Saharan Africa and is responsible for severe epidemic outbreaks.

salmonella_figure-finalIts unusual characteristics — including a high rate of lethality, invasiveness, atypical symptomatolgy and resistance to multiple antibiotics — are of rising concern.

In a new study, Cheryl Nickerson and her colleagues at the Biodesign Institute at Arizona State University and NASA Johnson Space Center demonstrate for the first time that this pathogen can cause lethal infections not only in humans but in mice, a finding which could potentially extend to other hosts as well.

The salmonella strain used in this study, D23580, belongs to a group of closely related strains collectively known as ST313, and was shown to more rapidly reach and colonize tissues of the spleen and gallbladder in mice, compared with a well-characterized “classic” salmonella strain.

In results appearing in the journal PLOS Neglected Tropical Diseases, lead authors Jiseon Yang and Jennifer Barrila also establish a critical variable of the pathogen known as LD50 — a measure of the median lethal dose (LD) necessary to produce a fatal infection — marking the first report of the entire natural course of disease for any ST313 strain.

Developing effective means to diagnose and treat deadly salmonella infections, including those caused by ST313, will require a more thorough understanding of the strategies used by such pathogens to infect the body. Establishing LD50 is a necessary step for examining the trajectory of salmonella infection and developing effective vaccines and therapies to combat it. 

“Despite being one of the best characterized pathogens, we still have limited knowledge of the mechanisms used by salmonella to cause disease in humans, including the multidrug-resistant ST313 isolates associated with rampant atypical disease and high mortality in sub-Saharan Africa,” said Nickerson, who is also a professor of microbiology at ASU’s School of Life Sciences.

The current study offers new insight into the virulence and pathogenesis properties of model ST313 strain, D23580, which shows both key similarities and differences between classic Typhimurium and Typhi strains in its virulence and pathogenesis-related properties, thus offering clues as to how it may cause disease in humans.

Thus far, no animal reservoir has been identified for ST313. Unlike conventional foodborne NTS infections, the transmission route for ST313 appears to be human-to-human. Genetic studies of iNTS strains obtained from Malawi, where ST313 is highly prevalent; indicate the strain may be losing genetic diversity, becoming a more specialized pathogen, similar to S. Typhi.

The current study, however, shows that ST313 strain D23580 could also infect mice and thus retains characteristics associated with classic NTS infection.  However, biochemical and phenotypic assays indicated that D23580 also exhibits important differences between classic NTS and typhoidal strains. Collectively, these results provide further evidence that this emerging pathogen is distinct from classic salmonella strains.

Kangeroos in South Africa? Bitlong meat strips contain meat from anything

I don’t know what bitlong is, but it’s apparently popular in South Africa and apparently it’s made from whatever meat is available.

Using DNA analysis on biltong, researchers found, according to the N.Y Times,  horse meat labeled as springbok, the native gazelle; giraffe meat biltong.mar.13labeled as the African antelope, kudu; and in an inexplicable case, kangaroo labeled as ostrich.

“For me the saddest finding was to find the Cape mountain zebra, an endangered species, being sold as biltong,” said Maria Eugenia D’Amato, a geneticist at the University of the Western Cape in South Africa and one of the authors of the study, in the journal Investigative Genetics.

From a total of 146 samples of biltong, sausage and minced meat, more than a hundred pieces of meat were mislabeled.

Beef was correctly labeled in all of the samples.

“Our biggest surprise was to find kangaroo in the samples,” Dr. D’Amato said. “This isn’t found anywhere on the continent, and it must have been imported.”

CHUCK DODD: In defense of food – not Pollan

Chuck Dodd, a veterinarian and PhD student at Kansas State University, writes:

I grew up in rural Missouri eating meat and potatoes, mostly meat, and quite a bit of it.

But my carnivorous mantra doesn’t match the advice of Michael Pollan, author of In Defense of Food—An Eaters Manifesto (right). He says:

“Eat food, not too much, mostly plants.”

Most of the world already follows Michael Pollan’s advice—out of necessity.

Approximately 4.7 billion people, or over two-thirds of the world’s population, live in lower income countries where safe food and water is limited. The Food and Agriculture Organization of the United Nations (FAO) now reports that rising food prices have contributed to a global increase in malnourishment and hunger. For people living in areas of poverty or conflict, it isn’t about food choices, it’s about simply eating. My wife, Lisa (with neighbor, left), and I lived among the poor in East Africa for six years. We’ve seen hunger, malnourishment, and the effects of diarrheal disease in children–not from the safe distance of a TV screen, but among our friends.  We strived to help transform lives in difficult places.       

Many of us who live in affluent societies enjoy abundant food choices. In the U.S., we have the luxury of being able to pick our diet based upon personal preference, individual nutrients, food production systems, origin, brand, and price. For those of us who have these abundant food choices, Pollan provides additional advice:

???don’t eat anything that your great grand-mother wouldn’t recognize as food;

???avoid food products containing ingredients that are a) unfamiliar, b) unpronounceable, c) more than five in number, or that include d) high-fructose corn syrup;

???avoid food products that make health claims;

???shop the peripheries of the supermarket and stay out of the middle. (processed food products dominate the center aisles); and,

???get out of the supermarket whenever possible.

Pollan’s recommendations are clever. But some of his other recommendations, like “pay more, eat less,” would offend our African friends, like Olendorrop (right).  Olendorrop faces daily challenges in feeding his family.  In the semi-arid savannah of the Rift Valley in northern Tanzania, he struggles to raise sheep and goats, grow corn, and survive.  He has learned how to use dewormers to keep his livestock healthy.  When he uses an antibiotic to treat a sick animal, he doesn’t care about organic food.  All of his animals are grass-fed because corn is people food.  He can’t go to the supermarket because there isn’t one.  He isn’t worried about health claims and ingredients because his food doesn’t have labels.  If Olendorrop paid more and ate less, his family wouldn’t survive.

My advice: if you can afford to choose what you eat, be thankful. Being able to consider what you eat is a luxury in itself. 

Our eater’s manifesto should be to help others simply eat.  Have we, the affluent with abundant food choices, finally arrived, or have we lost touch with global reality?  Do we really need to defend our food from food science and food production systems, as Pollan writes, or do we need to defend the 923 million undernourished people in the world  who don’t have food and help transform their lives?