Tag Archives: salmonella

New vaccine is incredibly efficient at preventing typhoid

Caused by the bacterium Salmonella Typhi, typhoid is a major cause of fever in children in low- and middle-income countries and is responsible for nearly 11 million cases and more than 116,000 deaths a year worldwide.

It is usually spread through contaminated food or water. Once Salmonella Typhi bacteria are eaten or drunk, they multiply and spread into the bloodstream. Symptoms include prolonged high fever, fatigue, headache, nausea, abdominal pain, and constipation or diarrhoea. Some patients may have a rash. Severe cases may lead to serious complications or even death. Salmonella Typhi lives only in humans.

In 2018, the World Health Organization (WHO) recommended the introduction of typhoid conjugate vaccine (TCV) for infants and children over six months of age in typhoid-endemic countries, and added it to its list of pre-qualified vaccines.

Prior to TCV, two vaccines have been used for many years to protect people from typhoid fever, an injectable vaccine based on the purified antigen for people aged over 2 years and a live attenuated oral vaccine in capsule formulation for people aged over 5 years. These vaccines do not provide long-lasting immunity and are not approved for children younger than 2 years old.

Although TCV has been shown to protect against the disease in studies involving healthy volunteers in the UK, no efficacy studies in endemic populations had been completed. Now, the Typhoid Vaccine Acceleration Consortium (TyVAC), which includes researchers from the University of Oxford, the University of Maryland School of Medicine, and PATH has completed a large field study in Nepal and published the interim analysis in the New England Journal of Medicine.

The study involved 20,000 children aged 9 months to 16 years of age, who were randomly given one of two vaccines: half received TCV and half received the Group A meningococcal (MenA) vaccine – the latter acted as the control group.

Blood tests showed that typhoid occurred in 7 participants who received TCV and 38 receiving Men A vaccine. The researchers noted that these were preliminary results, and that the study will continue to follow-up the participants for two years.

Dr. Andrew Pollard, Professor of Paediatric Infection and Immunity at Oxford University’s Department of Paediatrics, said: “This is the first study to show that a single dose of TCV is safe, immunogenic, and effective, which provides clear evidence that vaccination will help efforts to control this serious disease and is a strong endorsement of the WHO policy for vaccine implementation.”

“The efficacy of these results in an endemic population adds to a growing body of evidence supporting the use of TCV to reduce disease and save lives in populations that lack clean water and improved sanitation,” said Dr. Kathleen Neuzil, MD, MPH director of the Center for Vaccine Development and Global Health at the University of Maryland School of Medicine and director of TyVAC.

These results show the vaccine has the potential to significantly reduce the burden of typhoid in high-risk populations. This is especially timely with the recent spread of extensively drug-resistant typhoid, which threatens child health in affected regions.

Pakistan’s current typhoid outbreak is the first-ever reported outbreak of ceftriaxone-resistant typhoid and represents an alarming trend in the spread of drug-resistant typhoid. Not only is the strain resistant to ceftriaxone, the standard treatment in many parts of the world, but it is also resistant to most antibiotics commonly used for typhoid, making it increasingly challenging and costly to treat.

TCVs have the potential to overcome many of the challenges that impeded uptake of earlier vaccines, including longer-lasting protection, fewer doses, and suitability for children under two years of age, allowing for inclusion in routine childhood immunization programs.

Mysterious 16th-century Mexican Megadeath pathogen discovered

The Megadeath from 16th century Mexico is one of the biggest epidemiological mysteries of humankind. Now, researchers from at the Max Planck Institute for the Science of Human History might have finally solved it.

"Coronado sets out to the north" — oil painting by Frederic Remington Spanish Francisco Vázquez de Coronado Expedition (1540 - 1542), passing through Colonial New Mexico, to the Great Plains. Source: Wikipedia

“Coronado sets out to the north” — oil painting by Frederic Remington Spanish Francisco Vázquez de Coronado Expedition (1540 – 1542), passing through Colonial New Mexico, to the Great Plains. Source: Wikipedia

Between 1545 and 1576, epidemics of “cocoliztli” (Nahuatl for “pest”) were indigenous hemorrhagic fevers thought to be transmitted by rodent hosts and aggravated by extreme drought conditions.

Until recently, the only information scientists had about the killer pathogen was based on historical findings describing symptoms. Many scientists have correlated the wipe-out with the arrival of Spanish expeditors.

The research team applied a new method of investigation: a screening technique called the Metagenome Analyzer Alignment Tool, or MALT, which allows researchers to process millions of sequencing reads within hours and match these with known bacteria from a reference database.

Scientists took samples from an ancient graveyard in proximity to Oaxaca city. “Teeth are an excellent source of DNA,” says Kirsten Bos, an anthropologist at the Max Planck Institute for the Science of Human History who worked on the study. One important reason is that pathogens are well preserved by the enamel.

“The screening technique used here will be transformative for future work on archaeological disease — it’s no longer necessary to have a candidate pathogen in mind for molecular detection,” Bos said. “The flexibility offered by our approach is what’s needed to tackle many questions related to disease history and ecology, where you often don’t know what disease you’re looking for until you’ve found it.”

Åshild J. Vågene conducting lab work at the Max Planck Institute for the Science of Human History.
Credits: Elizabeth Nelson

“We intend to apply similar techniques to search for diseases in other archaeological samples from different time periods and locations. This technique opens so many doors for us to learn about disease in the past.” she added.
Researchers discovered that Salmonella enterica (the bacteria that cause paratyphoid fever) was present in the teeth of 11 people buried in a large Mixtec cemetery in southern Mexico.

Overview of Teposcolula-Yucundaa, showing its location in the Mixteca Alta region of Oaxaca, Mexico (A), and its central administrative area (B), where excavations took place. (C) shows a drawing of individual 35, from which an S. enterica genome was isolated.
Åshild J. Vågene et al. Salmonella enterica genomes from victims of a major 16th century epidemic in Mexico. Nature Ecology and Evolution.

Paratyphoid fever is caused by fecal contamination of food and water. Today, it usually encountered in poor, crowded places. It’s possible that the Spanish aggravated the spread by relocating people and instituting new agricultural practices.

“This specific pathogen may be one of several causes for the disease,” said Åshild Vågene, a co-author of the paper.

“We can only look for pathogens that we know exist today,” she added. “We can’t look for things that we don’t know existed.It’s the first piece of the puzzle to perhaps finding out what caused this epidemic mystery,” she concluded.

Evolution selects the most effective genes — even by a hundredth of a percent

Evolution promotes the survival of the most adept members of a species — but exactly how much “fitter” an organism has to be, compared to its peers, to hold a selective advantage over them? A new study from Uppsala University has measured the forces that shape bacterial genomes, and determined that a difference as tiny as one hundredth of a percent is sufficient to determine the winners and losers in the evolutionary race.

The go-to phrase when trying to explain evolution in a nutshell has to be “survival of the fittest.” Interestingly enough, the phrase was coined in 1864 by British philosopher Herbert Spencer to draw a parallel between his economic theories and Darwin’s work — it was only later adapted into the theory of evolution. But it does a pretty good job of explaining the general concept.

For example, in giraffes a longer necks represents an evolutionary advantage as it allows them to reach more food. Over time, nature selects against short-neck giraffes who, by contrast, are hard pressed to get enough to eat. They produce less offspring, have less energy to defend against predators, and eventually disappear along with the genes for short necks.

Image credits Richter Maganhildi.

Image credits Richter Maganhildi.

But the phrase does leave some questions unanswered; for example, how much longer has one giraffe’s neck have to be compared to the others’ to count as “fitter” in the eyes of evolution?

Professor Diarmaid Hughes and graduate student Gerrit Brandis set out to measure just that, by studying bacterial genomes. The team observed Salmonella in their experiments, but the mechanisms they investigated (such as competition for food, or the selective pressure to use that food to grow faster than their peers) hold true for all organisms.

In order to grow, bacteria must translate their genetic code into amino acids and then assemble them into proteins. Growth is thus bottle-necked by the the speed of translation. Genetic information also has ‘redundancy’, meaning that there are several different pieces of code (codons) that can be translated into any one amino acid.

Brandis and Hughes wanted to know whether it mattered which particular codons were used to make EF-Tu, one of the most important proteins in Salmonella. They altered the genetic makeup of the bacteria and found that switching even a single codon in the gene for this protein with any one of the alternative codons reduced the organism’s fitness. On average, changing a codon reduced the speed of expression by 0.01 percent per generation.

But even this tiny amount was enough to determine a selective advantage, creating a codon usage bias — the widespread use of particular codons to make highly expressed proteins. This bias is seen in nearly all fast-growing organisms, such as bacteria and yeasts that cause infections in humans.

Over hundreds of millions of years, translation mechanisms were shaped by evolution to be as efficiently as possible — and in the adaptation race, even a hundredth of a percent counts.

The full paper, titled “The Selective Advantage of Synonymous Codon Usage Bias in Salmonella” has been published online in the journal PLoS Genetics and can be read here.

A computer (PC) controls the motorized rotor that spins the disc, a laser that heats up chambers inside the disc, and a strobe light and camera (CCD) that snap pictures of the disc’s readout strip.

Spinning disk spots foods tainted with Salmonella in 30 minutes

Researchers in South Korea may have come across a novel and effective idea to tackle foods tainted with Salmonella bacteria. What looks like a disk actually contains six separate microfluidic slices that work together to provide DNA extraction, amplification, and detection in less than 30 minutes instead of days and a full-blown lab typically required for Salmonella detection.

A computer (PC) controls the motorized rotor that spins the disc, a laser that heats up chambers inside the disc, and a strobe light and camera (CCD) that snap pictures of the disc’s readout strip.

A computer (PC) controls the motorized rotor that spins the disc, a laser that heats up chambers inside the disc, and a strobe light and camera (CCD) that snap pictures of the disc’s readout strip. Credit: Analytical Chemistry

Salmonella causes an estimated 1.2 million illnesses and 450 deaths in the U.S. each year. While the FDA runs periodic tests on food, especially imports, some contaminated food slips by because there aren’t enough resources to check foods quite as thoroughly as possible. The standard test involves growing cultures in the lab and then checking for strains of microbes. This takes days, requires expensive machinery and trained staff.

The Salmonella Disk

Yoon-Kyoung Cho of Ulsan National Institute of Science & Technology believes shes and her team have devised a method that might dramatically sped up the process and save a lot of money. The disk is essentially a microfluidic chip comprised of six identical slices, each capable of performing the same test. A network of channels and chambers run through each slice  that carry out individual steps in the pathogen detection process. After a sample is added to the center of the device, the rotation of the disc forces the solution outward into the channels of each slice.

For their demonstration, the South Korean researchers spiked milk and butter with known amounts of Salmonella enteritidis colonies. Before loading either sample in the salmonella disk detector, the researchers first concentrated the bacteria by capturing them with magnetic beads coated in anti-Salmonella antibodies.

The beads were loaded in a machinery with rotating disk and laser, which was fired on the salmonella detector disk. The samples flow from chamber to chamber, expanded by the heat of the laser, until it reaches the DNA amplification chamber. Here DNA is amplified via a reaction called recombinase polymerase amplification using primers specific to a known Salmonella gene. The primers are decorated with two molecules that allow for detection of the DNA using reagents.

Eventually, the DNA hits a detection strip where the reagents mixed with the DNA cause a visible band of color to form. The researchers found they could detect as few as 100 colony-forming units of Salmonella in milk and 10 in butter. This isn’t perfect, as even one cell can cause disease, but it’s a promising first step in this direction.

Findings were reported in the journal Analytical Chemistry.


US spice imports are filthier than you might think

When you buy your spices, you might be getting more seasoning than you might expect. Why not get some free tiny fragments of insects, dirt or animal feces to go with your chilly? According to the  Food and Drug Administration spices entering the U.S. are nearly twice as likely as the average FDA-regulated foodstuff to contain Salmonella pathogens or unacceptable amounts of filth.  The FDA cites that roughly 12% of US spice imports exceed the “maximum levels of natural or unavoidable defects,” such as insect body parts and animal hair.

“Nearly all of the insects found in spice samples were stored product pests, indicating inadequate packing or storage conditions,” the agency wrote in report. “The presence of rodent hair without the root in spices generally is generally indicative of contamination by rodent feces.”

FDA’s study identified 14 outbreaks involving spices from 1973 to 2010 that resulted in 2,000 people reporting illnesses worldwide. The number of outbreaks may be low because people use small amounts of spices on food or cook the seasonings before eating, as well as safety measures taken by the industry, the agency said.

The maximum level of such unavoidable defects can be translated to roughly 170 insect fragments or 25 rodent hairs for a two-ounce jar of paprika, for instance. Anything below that is deemed acceptable by the FDA – in other words, all spices contain considerable filth. The infographic below does a good job of summarizing what you’ll find in your spice jar on average for various types of spice. If you can’t see  egregious filth, it’s because it’s cloaked as fragments.


Click for magnified view.

The huge bread nuking microwave machine. (c) BBC

Microwave technique makes bread last for 120 days, without chemical or other preservatives

Fresh sliced bread

About one in three breads is thrown away because it gets too tough and infected, and thus inedible, because of mold. Scientists at an American company have found a way to keep bread fresh for up to two months after they zapped it in a sophisticated microwave array. This killed the bacteria and fungi that lead to mold formation.

Typically, if not frozen, a loaf of bread may last for up to seven days. In a world where 15 million children die each year from hunger, the develop world throws away some 40% of its food. In money that’s $165bn in the US alone.

When bread is concerned, its biggest threat is mold, which is caused by a fungus called Rhizopus stolonifer. This fungus thrives off the moisture garnered from evaporated water from the bread, which is usually wrapped in plastic bags, ironically creating ideal conditions. Manufactures try to keep the bread unspoiled from as long as possible by adding preservatives, then add extra chemicals to compensate for the lack of taste.

The huge bread nuking microwave machine. (c) BBC

The huge bread nuking microwave machine. (c) BBC

An US based company called Microzap used a giant metallic microwave device that resembles an industrial production line to zap a slice of bread and kill the mold spores in around 10 seconds. The device is typically used to kill bacteria such as MRSA and salmonella, but the researchers discovered it works just as well for bread munching bacteria as well.

“We treated a slice of bread in the device, we then checked the mould that was in that bread over time against a control, ” Microzap chief executive Don Stull explained.

“And at 60 days it had the same mould content as it had when it came out of the oven.”

It won’t work at home

The machine isn’t quite like your home microwave oven, though, so you won’t be able to make this work for you.

“We introduce the microwave frequencies in different ways, through a slotted radiator. We get a basically homogeneous signal density in our chamber – in other words, we don’t get the hot and cold spots you get in your home microwave.”

The device seems like a godsend for bread manufactures around the world, since it would allow bread to last for a longer time, while also cutting back chemical use. Some are worried, however, that this might up the cost of bread in an already tight margin industry. In the end, it’s all up to the consumer. Hopefully nuked bread won’t stir them away from the shelf.

“We’ll have to get some consumer acceptance of that,” Stull said. “Most people do it by feel and if you still have that quality feel they probably will accept it. “

via BBC


Suicidal bacteria illustrates evolution of co-operation

Salmonella typhimurium; suicidal cells sacrifice for the greated good

Salmonella typhimurium; suicidal cells sacrifice for the greated good

Bacteria have sometimes behaviour that can amaze scientists, by its complexity and efficiency. Salmonella can commit suicide and help their “brothers” to establish infections that are more damaging, thus helping their species. But scientists believe they have found the answer to this surprising kamikaze behavior.

This phenomenon which is called self-destructive cooperation often helps Salmonella typhimurium and Clostridium difficile establish powerful “citadels” of infection in the gut. Scientists from Switzerland and Canada studied this type of developing an infection, and the team led by Martin Ackermann of ETH Zurich in Switzerland made some interesting discoveries.

The bacteria inflames the gut and causes an eradication of the microflora, which is a competition for resource. However, in this process they destroy other bacteria too (most of it actually). After this assault there is no competition for the few bacteria remaining, which charge on the gut, claiming their victory.

“We thought it was a very strange phenomenon,” says team member Wolf-Dietrich Hardt, also at ETH Zurich. “The bacteria in the gut lumen are genetically identical, but some of them are prepared to sacrifice themselves for the greater good. You could compare this act to Kamikaze fighter pilots of the Japanese army.”

This suicidal act is caused by a genetic configuration, which is expressed only in some ocasions, not in all. Only a part of the bacteria have this suicidal gene, less than a quarter. If all of them would carry it, all of them would commit suicide as a consequence. The team concluded that some cells sacrifice for the greater good, which is quite an inventive and effective way of achieving a goal.