Posts about bacteria

80% of the Antibiotics in the USA are Used in Agriculture and Aquaculture

Citing an overabundance in the use of antibiotics by the agriculture and aquaculture industries that poses a threat to public health, economics professor Aidan Hollis has proposed a solution in the form of user fees on the non-human use of antibiotics.

In a newly released paper published (closed science, sadly, so no link provide), Hollis and co-author Ziana Ahmed state that in the United States 80% of the antibiotics in the country are consumed in agriculture and aquaculture for the purpose of increasing food production.

This flood of antibiotics released into the environment – sprayed on fruit trees and fed to the likes of livestock, poultry and salmon, among other uses – has led bacteria to evolve, Hollis writes. Mounting evidence cited in the journal shows resistant pathogens are emerging in the wake of this veritable flood of antibiotics – resulting in an increase in bacteria that is immune to available treatments.

If the problem is left unchecked, this will create a health crisis on a global scale, Hollis says.

Hollis suggest that the predicament could be greatly alleviated by imposing a user fee on the non-human uses of antibiotics, similar to the way in which logging companies pay stumpage fees and oil companies pay royalties.

“Modern medicine relies on antibiotics to kill off bacterial infections,” explains Hollis. “This is incredibly important. Without effective antibiotics, any surgery – even minor ones – will become extremely risky. Cancer therapies, similarly, are dependent on the availability of effective antimicrobials. Ordinary infections will kill otherwise healthy people.”

Bacteria that can effectively resist antibiotics will thrive, Hollis adds, reproducing rapidly and spreading in various ways.

“It’s not just the food we eat,” he says. “Bacteria is spread in the environment; it might wind up on a doorknob. You walk away with the bacteria on you and you share it with the next person you come into contact with. If you become infected with resistant bacteria, antibiotics won’t provide any relief.”

While the vast majority of antibiotic use has gone towards increasing productivity in agriculture, Hollis asserts that most of these applications are of “low value.”

“It’s about increasing the efficiency of food so you can reduce the amount of grain you feed the cattle,” says Hollis. “It’s about giving antibiotics to baby chicks because it reduces the likelihood that they’re going to get sick when you cram them together in unsanitary conditions.

“These methods are obviously profitable to the farmers, but that doesn’t mean it’s generating a huge benefit. In fact, the profitability is usually quite marginal.

“The real value of antibiotics is saving people from dying. Everything else is trivial.”

While banning the use of antibiotics in food production is challenging, establishing a user fee makes good sense, according to Hollis.

Such a practice would deter the low-value use of antibiotics, with higher costs encouraging farmers to improve their animal management methods and to adopt better substitutes for the drugs, such as vaccinations.

Hollis also suggests that an international treaty could ideally be imposed. “Resistant bacteria do not respect national borders,” he says. He adds that such a treaty might have a fair chance of attaining international compliance, as governments tend to be motivated by revenue collection.

Hollis notes that in the USA, a move has been made to control the non-human use of antibiotics, with the FDA recently seeking voluntary limits on the use of antibiotics for animal growth promotion on farms.

Related: Raising Food Without AntibioticsOur Dangerous Antibiotic Practices Carry Great RisksWhat Happens If the Overuse of Antibiotics Leads to Them No Longer Working?Antibiotics Too Often Prescribed for Sinus Woes

Search for Antibiotic Solutions Continues: Killing Sleeper Bacteria Cells

Killing Sleeper Cells and Superbugs with Assassin Janitors

Discovered in 2005 by scientists from Bayer Healthcare in Germany, ADEP4 killed a variety of different bacteria and cured lethal infections in mice and rats.

Here’s how it works. Proteins need to fold into very precise shapes to do their jobs, and misfolded proteins are wastes of space. Bacteria dispose of these useless molecules with ClpP—a janitorial protein that digests other proteins. It works with a partner, which recognises misfolded proteins, unfolds them, and threads them through a hole in the middle of ClpP so they can be broken down. But ADEP4 opens ClpP up so it no longer needs its partner. The janitor now becomes an assassin, running amok and chopping up any protein it comes across, misfolded or not.

The Bayer scientists showed that ADEP4 can force fast-growing cells to self-destruct, but Lewis suspected that it would do the same to persisters. Afterall, ClpP’s partner requires energy to do its job, but ClpP itself doesn’t. Once ADEP4 opens it up, it should go about its fatal business even in a dormant cell.

Lewis’ team found that ADEP4 did effectively kills persister populations of Staphylococcus aureus, but the bacteria bounce back. ClpP isn’t essential, so the bacteria just inactivated it to evolve their way around ADEP4. This, says Lewis, is why Bayer stopped working on the drug.

His solution was to pair ADEP4 with another antibiotic called rifampycin. ADEP4 would kill off the majority of the persisters, and if any of the rest started growing again, rifampycin would finish them off. He predicted that the double-whammy would leave very few survivors, maybe just a thousand cells or so.

“That’s not what we saw,” he says. “What we saw was complete sterilisation.”

This is a very nice effort. As our efforts fail to find “magic bullet” antibiotics fail and antibiotic resistance increases combo drug solutions offer some hope. While this is good news, the overall state of our ability to treat bacterial infections continues to decline as our misuse of antibiotics has greatly increased the speed at which antibiotic resistance has developed in bacteria.

This solution only works on gram positive antibiotics. ADEP4 is too big to pass through the extra outer layers of the gram-negative bacteria like ecoli and salmonella.

Related: Entirely New Antibiotic Developed, Platensimycin (2006) (2013 update: Platensimycin is a very effective antibiotic in vivo when continuously administered to cells, however this efficacy is reduced when administered by more conventional means. Efforts continue to find a way to create delivery options that are successful in treating people.) – New Family of Antibacterial Agents Discovered (2009)Potential Antibiotic Alternative to Treat Infection (2012)

Go Slow with Genetically Modified Food

My thoughts on Genetically Modified Organisms (GMO), specifically GM foods, basically boil down to:

  • messing with genes could create problems
  • we tend to (and especially those seeking to gain an advantage tend to – even if “we” overall wouldn’t the people in the position to take aggressive measures do) ignore risks until the problems are created (often huge costs at that point)
  • I think we should reduce risk and therefore make it hard to justify using GMO techniques
  • I agree occasionally we should do so, like it seems with oranges and bananas.
  • I agree the practice can be explained in a way that makes it seem like there is no (or nearly no) risk, I don’t trust we will always refrain from stepping into an area where there is a very bad result

Basically I would suggest being very cautious with GMO. I like science and technology but I think we often implement things poorly. I think we are not being cautious enough now, and should reduce the use of GMO to critical needs to society (patents on the practices need to be carefully studied and perhaps not permitted – the whole patent system is so broken now that it should be questioned at every turn).

Antibiotic misuse and massive overuse is an obvious example. We have doctors practicing completely unjustified misuse of antibiotics and harming society and we have factory farms massively overusing antibiotics causing society harm.

The way we casually use drugs is another example of our failure to sensibly manage risks, in my opinion. This of course is greatly pushed by those making money on getting us to use more drugs – drug companies and doctors paid by those companies. The right drugs are wonderful. But powerful drugs almost always have powerful side effects (at least in a significant number of people) and those risks are multiplied the more we take (due to interactions, weakness created by one being overwhelmed by the next etc.). We should be much more cautious but again we show evidence of failing to act cautiously which adds to my concern for using GMO.

I love antibiotics, but the way we are using them is endangering millions of lives (that is a bad thing). I don’t trust us to use science wisely and safely. We need to more consciously put barriers in place to provent us creating massively problems.

Related: Research on Wheat RustThe AvocadoOverfishing, another example of us failing to effectively cope with systemic consequences

Scientific Inquiry Process Finds That Komodo Dragons Don’t have a Toxic Bite After All

This articles is another showing the scientific inquiry process at work. Scientists draw conclusions based on the data they have and experiments they do. Then scientists (sometimes the same people that did the original work) seek to confirm or refute the initial conclusions (based on new evidence or just repeating a similar experiment) and may seek to extend those conclusions.

Sometimes the scientists conclude the initial understanding was incorrect, such as with Komodo Dragon’s: Here Be Dragons: The Mythic Bite of the Komodo

for centuries Komodos have been feared by many, with tales of their deadly bite echoing through local cultures. It’s even thought the monstrous lizards may have inspired the mythical beasts that share their name. Their villainous reputation only grew when these fearsome predators were discovered by Europeans in the early twentieth century. But of all the terrible tales told about these dragons, none has been so persistent and pervasive than that of their bite. The mouths of Komodos are said to be laden with deadly bacteria from the decaying corpses they feed on, microbes so disgustingly virulent that the smallest bite lethally infects prey. As the story goes, Komodos have turned oral bacteria into a venom.

It’s a truly fascinating way for an animal to feed — well, truly fascinating in that it’s not true at all.

Related: Video of Young Richard Feynman Talking About Scientific ThinkingNanoparticles With Scorpion Venom Slow Cancer SpreadBig Lizards in Johor BahruNigersaurus

People are Superorganisms With Microbiomes of Thousands of Species

In a recent article in National Geographic Carl Zimmer has again done a good job of explaining the complex interaction between our bodies and the bacteria and microbes that make us sick, and keep us healthy.

The damage done by our indiscriminate use of antibiotics is not just the long term resistance that we create in bacteria (making the future more dangerous for people) that I have written about numerous times but it also endangers the person taking the anti-biotics in the short term. Sometimes the other damage is a tradeoff that should be accepted. But far too often we ignore the damage taking antibiotics too often does.

When You Swallow A Grenade

While antibiotics can discriminate between us and them, however, they can’t discriminate between them and them–between the bacteria that are making us sick and then ones we carry when we’re healthy. When we take a pill of vancomycin, it’s like swallowing a grenade. It may kill our enemy, but it kills a lot of bystanders, too.

If you think of the human genome as all the genes it takes to run a human body, the 20,000 protein-coding genes found in our own DNA are not enough. We are a superorganism that deploys as many as 20 million genes.

Before he started taking antibiotics, the scientists identified 41 species in a stool sample. By day 11, they only found 13. Six weeks after the antibiotics, the man was back up to 38 species. But the species he carried six weeks after the antibiotics did not represent that same kind of diversity he had before he took them. A number of major groups of bacteria were still missing.

They found that children who took antibiotics were at greater risk of developing inflammatory bowel disease later in life. The more antibiotics they took, the greater the risk. Similar studies have found a potential link to asthma as well.

The human body contains trillions of microorganisms — outnumbering human cells by 10 to 1. Because of their small size, however, microorganisms make up only about 1% to 3% of the body’s mass, but play a vital role in human health.

Where doctors had previously isolated only a few hundred bacterial species from the body, Human Microbiome Project (HMP) researchers now calculate that more than 10,000 microbial species occupy the human ecosystem. Moreover, researchers calculate that they have identified between 81% and 99% of all microorganismal genera in healthy adults.

“Humans don’t have all the enzymes we need to digest our own diet,” said Lita Proctor, Ph.D., NHGRI’s HMP program manager. “Microbes in the gut break down many of the proteins, lipids and carbohydrates in our diet into nutrients that we can then absorb. Moreover, the microbes produce beneficial compounds, like vitamins and anti-inflammatories that our genome cannot produce.” Anti-inflammatories are compounds that regulate some of the immune system’s response to disease, such as swelling.

“Enabling disease-specific studies is the whole point of the Human Microbiome Project,” said Barbara Methé, Ph.D., of the J. Craig Venter Institute, Rockville, MD, and lead co-author of the Nature paper on the framework for current and future human microbiome research. “Now that we understand what the normal human microbiome looks like, we should be able to understand how changes in the microbiome are associated with, or even cause, illnesses.”

Read the full NIH press release on the normal bacterial makeup of the body

Related: Tracking the Ecosystem Within UsWhat Happens If the Overuse of Antibiotics Leads to Them No Longer Working?Antibacterial Products May Do More Harm Than GoodAntibiotics Too Often Prescribed for Sinus Woes

Human Gene Origins: 37% Bacterial, 35% Animal, 28% Eukaryotic

The percent of human genes that emerged in various stages of evolution: 37% bacterial, 28% eukaryotic, 16% animal, 13% vertebrate, 6% primate. The history that brought us to where we are is amazing. Eukaryotes include animals, plants, amoebae, flagellates, amoeboflagellates, fungi and plastids (including algae). So eukaryotic genes are those common to us and other non-animal eukaryotes while those classified as animal genes are shared by animals but not non-animal eukaryotes.

We are living in a bacterial world, and it’s impacting us more than previously thought by Lisa Zyga

Bacterial signaling is not only essential for development, it also helps animals maintain homeostasis, keeping us healthy and happy. As research has shown, bacteria in the gut can communicate with the brain through the central nervous system. Studies have found that mice without certain bacteria have defects in brain regions that control anxiety and depression-like behavior. Bacterial signaling also plays an essential role in guarding an animal’s immune system. Disturbing these bacterial signaling pathways can lead to diseases such as diabetes, inflammatory bowel disease, and infections. Studies also suggest that many of the pathogens that cause disease in animals have “hijacked” these bacterial communication channels that originally evolved to maintain a balance between the animal and hundreds of beneficial bacterial species.

Scientists have also discovered that bacteria in the human gut adapts to changing diets. For example, most Americans have a gut microbiome that is optimized for digesting a high-fat, high-protein diet, while people in rural Amazonas, Venezuela, have gut microbes better suited for breaking down complex carbohydrates. Some people in Japan even have a gut bacterium that can digest seaweed. Researchers think the gut microbiome adapts in two ways: by adding or removing certain bacteria species, and by transferring the desired genes from one bacterium to another through horizontal gene transfer. Both host and bacteria benefit from this kind of symbiotic relationship, which researchers think is much more widespread than previously thought.

We want badly for the message in ‘Animals in a bacterial world,’ to be a call for the necessary disappearance of the old boundaries between life science departments (e.g., Depts of Zoology, Botany, Microbiology, etc.) in universities, and societies (e.g., the American Society for Microbiology, etc.). We also want the message disseminated in college and university classes from introductory biology to advanced courses in the various topic areas of our paper.”

Very cool stuff. This amazing facts scientists discover provide an amazing view of the world we live in and how interconnected we are to other life forms in ways we don’t normally think of.

Related: People’s Bodies Carry More Bacterial Cells than Human CellsMicrobes Flourish In Healthy PeopleTracking the Ecosystem Within UsForeign Cells Outnumber Human Cells in Our BodiesBacteria Beneficial to Human Health

Scientific Illiteracy Leads to Failure to Vaccinate Which Leads to Death

Anti-vaccination propagandists help create the worst whooping cough epidemic in 70 years by Steven Salzberg is a professor at Johns Hopkins School of Medicine:

When the vaccination rates drop, everyone becomes more vulnerable to infectious diseases. When more than 90% of the population is vaccinated, we have “herd immunity” – this means the disease can’t spread because there aren’t enough susceptible people in the community. So the high rate of vaccine refusal in Washington makes it easier for whooping cough (and other diseases) to spread.

And now we learn that the U.S. is in the midst of the worst whooping cough epidemic in 70 years. One of the most hard-hit states is Washington, which the CDC just announced (on 20 July) has suffered 2,520 cases so far this year, a 1300% increase over last year. This is the highest number of cases reported in Washington since 1942.

The U.S. has had over 17,000 cases this year, putting it on track for the worst year since 1959. The highest rate of infection in the nation is in Wisconsin (which has also been hit hard by anti-vaccine effects), followed by Washington and Montana. 10 deaths have been reported, mostly in infants who were too young to be vaccinated. For all this, we can thank the anti-vaccination movement.

The failure of our society to appreciate the value of science has dire consequences. We are lucky to benefit from the results of scientific advances around us everyday. Some people, instead of appreciating the value of science waste these great gifts we have been given.

What people want to believe is up to them. When people’s actions risk others lives that is not ok. Drunk drivers risk others lives; therefore we don’t allow drunk driving. Society requires that people respect others right to live. It is sensible to require people to cooperate to limit damaging behavior: such as drunk driving or not being properly vaccinated.

Pertussis (whooping cough) is a highly contagious bacterial disease that causes uncontrollable, violent coughing. The coughing can make it hard to breathe. Pertussis, or whooping cough, is an upper respiratory infection caused by the Bordetella pertussis or Bordetella parapertussis bacteria. It is a serious disease that can cause permanent disability in infants, and even death.

Related: Vaccines Can’t Provide Miraculous Results if We Don’t Take ThemDeadly Choices: How the Anti-Vaccine Movement Threatens Us All (book)CDC Report on Failures to VaccinateOur Dangerous Antibiotic Practices Carry Great Risks

Our Dangerous Antibiotic Practices Carry Great Risks

Our continued poor antibiotics practices increase the risk of many deaths. We are very poor at reacting to bad practices that will kill many people in the future. If those increased deaths happened today it is much more likely we would act. But as it is we are condemning many to have greatly increased odds of dying from bacterial causes that could be prevented if we were more sensible.

Resistance to antibiotics is becoming a crisis

Increasingly, microbes are becoming untreatable. Margaret Chan, director general of the World Health Organization, warned in March of a dystopian future without these drugs. “A post-antibiotic era means, in effect, an end to modern medicine as we know it,” she said. “Things as common as strep throat or a child’s scratched knee could once again kill.”

evidence is mounting that antibiotics are losing efficacy. Through the relentless process of evolution, pathogens are evading the drugs, a problem known broadly as antimicrobial resistance.

Europe has launched a $741 million, seven-year, public-private collaborative research effort to accelerate drug development.

Seeking new antibiotics is wise but the commentary completely ignores our bad practices that are causing the problem to be much worse than it would be if we acted as though bad practices that will lead to many deaths should be avoided.

Previous posts about practices we taking that create great risk for increased deaths: Antibiotics Too Often Prescribed for Sinus Woes (2007)Meat Raised Without Antibiotics is Sadly Rare Today (2007)Overuse of Antibiotics (2005)CDC Urges Increased Effort to Reduce Drug-Resistant Infections (2006)FDA May Make Decision That Will Speed Antibiotic Drug Resistance (2007)Antibacterial Soaps are Bad (2007)Waste Treatment Plants Result in Super Bacteria (2009)Antibiotics Breed Superbugs Faster Than Expected (2010)Antibiotics Use in Farming Can Create Superbugs (2010)What Happens If the Overuse of Antibiotics Leads to Them No Longer Working? (2011)Dangerous Drug-Resistant Strains of TB are a Growing Threat (2012)

Obviously bacteria evolve to survive the counter measures we currently have. The foolish practices of promoting ignorance of evolution leads to a society where the consequences of actions, and the presence of evolution, lead to bad consequences. We find ourselves in that society.

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The Appendix Serves As a Reservoir of Beneficial Bacteria

This is an interesting explanation for the purpose of the appendix.

The appendix does have a use – re-booting the gut

The US scientists found that the appendix acted as a “good safe house” for bacteria essential for healthy digestion, in effect re-booting the digestive system after the host has contracted diseases such as amoebic dysentery or cholera, which kill off helpful germs and purge the gut.

This function has been made obsolete by modern, industrialised society; populations are now so dense that people pick up essential bacteria from each other, allowing gut organisms to regrow without help from the appendix, the researchers said.

But in earlier centuries, when vast tracts of land were more sparsely populated and whole regions could be wiped out by an epidemic of cholera, the appendix provided survivors with a vital individual stockpile of suitable bacteria.

Related: Microbes Flourish In Healthy PeopleBeneficial BacteriaForeign Cells Outnumber Human Cells in Our Bodies

Using Nanocomposites to Improve Dental Filling Performance

After a dentist drills out a decayed tooth, the cavity still contains residual bacteria. Professor Huakun (Hockin) Xu says it is not possible for a dentist to remove all the damaged tissue, so it’s important to neutralize the harmful effects of the bacteria, which is just what the new nanocomposites are able to do.

Rather than just limiting decay with conventional fillings, the new composite he has developed is a revolutionary dental weapon to control harmful bacteria, which co-exist in the natural colony of microorganisms in the mouth.

“Tooth decay means that the mineral content in the tooth has been dissolved by the organic acids secreted by bacteria residing in biofilms or plaques on the tooth surface. These organisms convert carbohydrates to acids that decrease the minerals in the tooth structure,” says Xu, director of the Division of Biomaterials and Tissue Engineering in the School’s Department of Endodontics, Prosthodontics and Operative Dentistry.

The researchers also have built antibacterial agents into primer used first by dentists to prepare a drilled-out cavity and into adhesives that dentists spread into the cavity to make a filling stick tight to the tissue of the tooth. “The reason we want to get the antibacterial agents also into primers and adhesives is that these are the first things that cover the internal surfaces of the tooth cavity and flow into tiny dental tubules inside the tooth,” says Xu.

The main reason for failures in tooth restorations, says Xu, is secondary caries or decay at the restoration margins. Applying the new primer and adhesive will kill the residual bacteria, he says.

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Bacteria In Cave Isolated for 4 Million Years Highly Resistant to Many Antibiotics

PLoS published an interesting open access research paper on bacteria and their resistance to antibiotics. I am surprised how widespread and strong the antibiotic resistance was is the isolated bacteria that were studied. It raises more interesting questions about the important area of antibiotics.

The lead researcher on this study, Gerry Wright, previously published on antibiotic properties of bacteria found in soil.

Abstract of Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome

Antibiotic resistance is a global challenge that impacts all pharmaceutically used antibiotics. The origin of the genes associated with this resistance is of significant importance to our understanding of the evolution and dissemination of antibiotic resistance in pathogens. A growing body of evidence implicates environmental organisms as reservoirs of these resistance genes; however, the role of anthropogenic use of antibiotics in the emergence of these genes is controversial.

We report a screen of a sample of the culturable microbiome of Lechuguilla Cave, New Mexico, in a region of the cave that has been isolated for over 4 million years. We report that, like surface microbes, these bacteria were highly resistant to antibiotics; some strains were resistant to 14 different commercially available antibiotics. Resistance was detected to a wide range of structurally different antibiotics including daptomycin, an antibiotic of last resort in the treatment of drug resistant Gram-positive pathogens.

Enzyme-mediated mechanisms of resistance were also discovered for natural and semi-synthetic macrolide antibiotics via glycosylation and through a kinase-mediated phosphorylation mechanism. Sequencing of the genome of one of the resistant bacteria identified a macrolide kinase encoding gene and characterization of its product revealed it to be related to a known family of kinases circulating in modern drug resistant pathogens. The implications of this study are significant to our understanding of the prevalence of resistance, even in microbiomes isolated from human use of antibiotics. This supports a growing understanding that antibiotic resistance is natural, ancient, and hard wired in the microbial pangenome.

Related: Alligator Blood Provides Strong Resistance to Bacteria and VirusesBacteria Survive On All Antibiotic DietClay Versus MRSA Superbug

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