Superbugs have an arsenal of defences — but we’ve found a new way around them



Superbug Acinetobacter baumannii captured by an electron microscope.
Janice Carr/Centers for Disease Control and Prevention

Fernando Gordillo-Altamirano, Monash University and Jeremy J. Barr, Monash University

Researchers have not discovered any new antibiotics in decades. But our new research, published today in Nature Microbiology, has found a way to give a second wind to the antibiotics we do have.

It involves the use of viruses that kill bacteria.

The problem

Hospitals are scary, and the longer you remain in them, the greater your risk. Among these risks, hospital-acquired infections are probably the biggest. Each year in Australia, 180,000 patients suffer infections that prolong their hospital stays, increase costs, and sadly, increase the risk of death.

It sounds absurd — hospitals are supposed to be the cleanest of places. But bacteria are everywhere and can adapt to the harshest of environments. In hospitals, our increased use of disinfectants and antibiotics has forced these bacteria to evolve to survive. These survivors are called “superbugs”, with an arsenal of tools to resist antibiotics. Superbugs prey on the most vulnerable patients, such as those in intensive care units.

Acinetobacter baumannii is a superbug responsible for up to 20% of infections in intensive care units. It attaches to medical devices such as ventilator tubes and urinary and intravenous catheters. It causes devastating infections in the lungs, urinary tract, wounds and bloodstream.

Treatment is difficult because A. baumannii can produce enzymes that destroy entire families of antibiotics. Other antibiotics never make it past its outer layer, or capsule. This outer layer — thick, sticky, viscous and made of sugars — also protects the superbug from the body’s immune system. In some cases, not even the strongest — and most toxic — antibiotics can kill A. baumannii. As a result, the World Health Organisation named it a critical priority for the discovery of new treatments.




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A (somewhat) new solution

It’s said that the enemy of your enemy is your friend. Do bacteria have enemies?

Bacteriophages (or phages, for short) are the natural predators of bacteria. Their name literally means “bacteria eater”. You can find phages wherever you can find bacteria.

Phages are viruses. But don’t let that scare you. Unlike famous viruses — such as HIV, smallpox or SARS-CoV-2, the coronavirus that causes COVID — phages cannot harm humans. They only infect and kill bacteria. In fact, phages are quite picky. A single phage normally infects only one type of bacteria.

Electron micrograph image of multiple bacteriophages attached to a bacterial cell wall
Phages attach to the outside of bacteria, initiating the killing process.
Dr Graham Beards/Wikimedia Commons, CC BY-SA

Since their discovery in the early 1900s, doctors thought of an obvious use for phages: treating bacterial infections. But this practice, known as phage therapy, was largely dismissed after the discovery of antibiotics in the 1940s.

Now, with the alarming rise of antibiotic-resistant superbugs, and a lack of new antibiotics, researchers are revisiting phage therapy. In Australia, for example, a team lead by Professor Jon Iredell at Sydney’s Westmead Hospital reported in February the safe use of phage therapy in 13 patients suffering from infections by another superbug, Staphylococcus aureus.

We began our study by “hunting” for phages against A. baumannii. From waste water samples sourced from all over Australia, we successfully isolated a range of phages capable of killing the superbug. That was the easy part.

Erasing antibiotic-resistance

When mixing our phages with A. baumannii in the laboratory, they were able to wipe out almost the entire bacterial population. But “almost” was not good enough. Within a few hours, the superbug showed how wickedly smart it is. It had found a way to become resistant to the phages and was happily growing in their presence.

We decided to take a closer look at these phage-resistant A. baumannii. Understanding how it outsmarted the phages might help us choose our next attack.

We discovered that phage-resistant A. baumannii was missing its outer layer. The genes responsible for producing the capsule had mutated. Under the microscope, the superbug looked naked, with no sign of its characteristic thick, sticky and viscous surface.

To kill their bacterial prey, phages first need to attach to it. They do this by recognising a receptor on the surface of the bacteria. Think of it as a lock-and-key mechanism. Each phage has a unique key, that will only open the specific lock displayed by certain bacteria.

Our phages needed A. baumannii‘s capsule for attachment. It was their prospective port of entry into the superbug. When attacked by our phages, A. baumannii escaped by letting go of its capsule. As expected, this helped us decide our next attack: antibiotics.

We tested the action of nine different antibiotics on the phage-resistant A. baumannii. Without the protective capsule, the superbug completely lost its resistance to three antibiotics, reducing the dosage needed to kill the superbug. Phages had pushed the superbug into a corner.

We established a way to revert antibiotic-resistance in one of the most dangerous superbugs.

Looking forward

Phage therapy has already been used in patients with life-threatening A. baumannii infections, with successful results. This study highlights the possibility of using phages to rescue antibiotics, and to use them in combination. After all, two is better than one.The Conversation

Fernando Gordillo-Altamirano, Medical Doctor, PhD Student, School of Biological Sciences, Monash University and Jeremy J. Barr, Senior Lecturer in School of Biological Sciences, Microbiology, Monash University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

‘Deeply worrying’: 92% of Australians don’t know the difference between viral and bacterial infections


Paul De Barro, CSIRO

We are four months into a global virus outbreak, and public health awareness could well be at an all-time high. Which is why it is astonishing to discover that 92% of Australians don’t know the difference between a viral infection and a bacterial one.

The statistic comes from a survey carried out by CSIRO in March to inform our work on the OUTBREAK project – a multi-agency mission aimed at preventing outbreaks of antibiotic-resistant bacterial infections.

Our survey of 2,217 people highlights a disturbing lack of knowledge about germs and antibiotics. It reveals 13% of Australians wrongly believe COVID-19, a viral disease, can be treated with antibiotics, which target bacteria.




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More than a third of respondents thought antibiotics would fix the ‘flu or a sore throat, while 15% assumed antibiotics were effective against chicken pox or diarrhoea.

While 25% of those surveyed had never heard of antibiotic resistance, 40% admitted having taken antibiotics that didn’t clear up an infection. And 14% had taken antibiotics as a precaution before travelling overseas, despite this being unnecessary and ineffective for warding off holiday ailments.

Fuelling the rise of superbugs

The results are deeply worrying, because people who do not understand how antibiotics work are more likely to misuse or overuse them. This in turn fuels the rise of drug-resistant bacteria (also known as “superbugs”) and life-threatening infections.

While COVID-19 has brought the economy to its knees, superbugs pose economic challenges too. Australian hospitals already spend more than A$11 million a year treating just two of the most threatening drug-resistant infections, ceftriaxone-resistant E. coli and methicillin-resistant MRSA.

Without effective antibiotics, thousands more people will die from sepsis and people will be sicker for longer, slashing the size of the workforce and productivity. By 2050, drug-resistant bacteria are forecast to cost the nation at least A$283 billion and kill more people than cancer.




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Explainer: what are superbugs and how can we control them?


One crucial way to stop this is to improve public understanding of the value of antibiotics. Antibiotics that lose their effectiveness are very difficult to replace, so they need to be treated with respect.

Almost all today’s antibiotics were developed decades ago and, of the 42 antibiotics under development worldwide, only five are considered truly new, and only one targets bacteria of greatest drug-resistance concern.

No time to waste

We don’t know the full impact of drug-resistant bacteria in Australia. With about 75% of emerging infectious diseases coming from animals, there is no time to waste in getting a better understanding of how superbugs are spreading between humans, the environment and animals. That’s where the OUTBREAK project comes in.

This network, led by the University of Technology Sydney, uses artificial intelligence to analyse an immense amount of human, animal and environmental data, creating a nationwide system that can predict antibiotic-resistant infections in real time. It maps and models responses and provides important information to doctors, councils, farmers, vets, water authorities, and other stakeholders.

OUTBREAK offers Australia a unique opportunity to get on the front foot against superbugs. It would save millions of lives and billions of dollars, and could even be scaled globally.

Alongside this high-tech response, we need Australians to get to know their germs, and stop taking antibiotics unnecessarily. Without antibiotics, we may find ourselves facing a host of new incurable diseases, even as the world grapples with COVID-19.The Conversation

Paul De Barro, Senior Principal Research Scientist, Ecosystem Sciences, CSIRO

This article is republished from The Conversation under a Creative Commons license. Read the original article.

We can reverse antibiotic resistance in Australia. Here’s how Sweden is doing it



More stringent use of antibiotics is needed to curb antibiotic resistance. But how can we achieve this?
From shutterstock.com

Mina Bakhit, Bond University; Chris Del Mar, Bond University, and Helena Kornfält Isberg, Lund University

The antibiotic resistance threat is real. In the years to come, we will no longer be able to treat and cure many infections we once could.

We’ve had no new classes of antibiotics in decades, and the development pipeline is largely dry. Each time we use antibiotics, the bacteria in our bodies become more resistant to the few antibiotics we still have.

The problem seems clear and the solution obvious: to prescribe our precious antibiotics only when absolutely needed. Implementing this nationally is not an easy task. But Australia could take cues from other countries making significant progress in this area, such as Sweden.




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The Swedish example

Antibiotic use was rising steadily in Sweden during the 1980s and 1990s, causing an increase in antibiotic resistant bacteria. A group of doctors mobilised to tackle this threat, and brought together peak bodies across pharmaceuticals, infectious diseases and other relevant areas to form a national coalition.

The Swedish Strategic Programme Against Antibiotic Resistance (Strama) was founded in 1995.

Since then, Strama has been working on a national and regional level to reduce antibiotic use. Between 1992 and 2016, the number of antibiotics prescriptions decreased by 43% overall. Among children under four, antibiotics prescriptions fell by 73%.

Levels of antibiotic use and resistance in Sweden are now among the lowest of all OECD countries, both in humans and animals.

What has Australia done so far – and what more can we do?

In 2017, Australia’s chief medical officer sent a letter to all high-prescribing general practitioners. Over the following six months, this resulted in around a 10% reduction in antibiotic prescriptions among those GPs.

While an excellent start, this is just one of several interventions needed to avert the looming antibiotic crisis.




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Drug resistance: how we keep track of whether antibiotics are being used responsibly


Audit and feedback

The idea of audit and feedback sees GPs provided with a summary of their antibiotic prescribing rates over a specified period of time.

In Australia, antibiotic prescribing data are currently collected by the Pharmaceutical Benefits Scheme (PBS) and periodically used by the National Prescribing Service (NPS MedicineWise) to provide feedback to some GPs.

In Sweden, regular meetings between local Strama members and primary health care clinics serve to reinforce treatment guidelines. Strama representatives review individual doctors’ antibiotic prescribing as well as trends across the area, and discuss targets for optimal prescribing.

This results in some decrease in antibiotic use; a small but desirable effect if combined with other interventions.

Restrict access to specific antibiotics

The Australian Commission on Safety and Quality in Health Care keeps a list of antibiotics that should only be used as a last line of defence. An example is meropenem, which is commonly used to treat infections with multidrug-resistant organisms such as septicaemia.

Current restrictions stipulate these antibiotics can only be used in hospitals under the supervision of a hospital antimicrobial stewardship team. This team usually consists of an infectious disease specialist, a microbiologist and a pharmacist. The team reviews the request and either approves it or recommends using another antibiotic.

Strama takes a similar approach.

But the way this is enforced differs between Australian hospitals. We may need to strengthen these restrictions if resistance continues to increase.

Doctors can educate patients about when antibiotics are and aren’t appropriate.
From shutterstock.com

Stop default repeat prescriptions

Prescriptions which include a “repeat” could leave patients believing another course of antibiotics is needed, when this is not always the case. They may hold on to the prescription with a “just in case” attitude to take when they feel it’s necessary, or even give the prescription to someone else.

In Sweden, there are no default repeat prescriptions for antibiotics and this is reinforced by appropriate package size.




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Pleasingly, Australia’s Pharmaceutical Benefits Advisory Committee has recently recommended the removal of default repeat options for a range of common antibiotics in high usage, where no repeats are deemed clinically necessary.

Delayed prescribing

Delayed prescribing is when a GP provides a prescription during the consultation, but advises the patient to see if the symptoms will resolve first before using it (a “wait-and-see” approach).

GPs use delayed prescribing in situations of uncertainty as a safety measure, or when patients appear anxious and require additional assurance antibiotics are accessible in case the infection gets worse.

A systematic review found delayed prescribing resulted in 31% of people taking the course of antibiotics compared to 93% who were prescribed them normally.

In Sweden, national treatment guidelines for common infections in primary health care support GPs delaying antibiotic prescribing.

Public engagement

To change public attitudes around antibiotic use and preservation, it’s important to communicate the negative effects of the unnecessary use of antibiotics and the risk of antibiotic resistance for the individual as well as the community.

Continuous awareness campaigns are essential (for example, via the media) to keep the public tuned in to the issue. The French campaign “antibiotics are not automatic” is a good example.




Read more:
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Further, enabling patients to be involved in the decision of whether to use antibiotics or not encourages discussion between the doctor and the patient around the benefits and harms of potential treatments. Using shared decision making in consultations has proven effective in reducing antibiotic prescribing by about one-fifth.

Each of these strategies contributes a small amount to improving antibiotic usage. Like the Swedish Strama program, the combination will need to be sustained and reinforced over many years to reach levels of antibiotic use comparable to the lowest prescribing OECD countries, like Sweden.The Conversation

Mina Bakhit, Postdoctoral Research Fellow, Bond University; Chris Del Mar, Professor of Public Health, Bond University, and Helena Kornfält Isberg, MD, General practitioner, PhD-student, Lund University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Antibiotic resistance is not new – it existed long before people used drugs to kill bacteria



Antibiotic resistance can spread between microbes within hours.
Lightspring/Shutterstock.com

Ivan Erill, University of Maryland, Baltimore County

Imagine a world where your odds of surviving minor surgery were one to three. A world in which a visit to the dentist could spell disaster. This is the world into which your great-grandmother was born. And if humanity loses the fight against antibiotic resistance, this is a world your grandchildren may well end up revisiting.

Antibiotics changed the world in more ways than one. They made surgery routine and childbirth safer. Intensive farming was born. For decades, antibiotics have effectively killed or stopped the growth of disease-causing bacteria. Yet it was always clear that this would be a rough fight. Bacteria breed fast, and that means that they adapt rapidly. The emergence of antibiotic resistance was predicted by none other than Sir Alexander Fleming, the discoverer of penicillin, less than a year after the first batch of penicillin was mass produced.

Yet, contrary to popular belief, antibiotic resistance did not evolve recently, or in response to our use and misuse of antibiotics in humans and animals. Antibiotic resistance first evolved millions of years ago, and in the most mundane of places.

I am a bioinformatician, and my lab studies the evolution of bacterial genomes. With antibiotic resistance becoming a major threat, I’m trying to figure out how resistance to antibiotics emerges and spreads among bacterial populations.

A billion-years-old arms race

Most antibiotics are naturally produced by bacteria living in soil. They produce these deadly chemical compounds to fend off competing species. Yet, in the long game that is evolution, competing species are unlikely to sit idly by. Any mutant capable of tolerating a minimal quantity of the antibiotic will have a survival advantage and will be selected for – over generations this will produce organisms that are highly resistant.

So it’s a foregone conclusion that antibiotic resistance, for any antibiotic researchers might ever discover, is likely already out there. Yet people keep talking about the evolution of antibiotic resistance as a recent phenomenon. Why?

Resistance can and does evolve when bacteria are persistently exposed to a new antibiotic they have never encountered. Let’s call this the old-fashioned evolutionary road. Second, when bacteria are exposed to a novel antibiotic and are in contact with bacteria already resistant to this antibiotic, it is just a matter of time before they get cozy and trade genes. And, importantly, once genes have been packaged for trading, they become easier and easier to share. Bacteria then meet other bacteria, which meet more bacteria, until one of them eventually meets you.

Bacteria can evolve resistance to high levels of antibiotics in just days.

The rise and fall of sulfa drugs

For all their might, antibiotics are not the only substances capable of effectively killing bacteria (without killing us). A decade before the mass production of penicillin, sulfonamide drugs became the first commercial antibacterial agent. Sulfa drugs act by blocking an enzyme – called DHPS – that is essential for bacteria to grow and multiply.

Sulfa drugs are not antibiotics. No known organism produces them. They are chemotherapeutic agents synthesized by humans. No natural producer means no billion-year-old arms race and no pool of ancient resistance genes. We would expect bacteria to evolve resistance to sulfa drugs via the good old-fashioned way. And they did.

Just a few years after their commercial introduction, the first cases of resistance to sulfa drugs were reported. Mutations to the bacterial DHPS enzyme made sulfa drugs ineffective. Then penicillin and the antibiotic era came about. Sulfa drugs were relegated to a secondary role in medicine, but they gained popularity as cheap antimicrobials in animal husbandry. By the 1980s resistance to sulfa drugs was rampant and worldwide. What had happened?

At odds with resistance

To answer this question our research team took sequences of sulfa drug resistance genes from disease-causing bacteria and compared them to millions of “normal” versions of the DHPS enzyme in nonpathogenic bacteria.

The team identified two large groups of bacteria that had DHPS enzymes resistant to sulfa drugs. By studying their DNA sequences, we were able to show that these resistant DHPS enzymes had been present in these two groups of bacteria for at least 500 million years. Yet sulfa drugs were first synthesized in the 1910s. How could resistance be around 500 million years ago? And how did these resistance genes find their way into the disease-causing bacteria plaguing hospitals worldwide?

The clues left in gene sequences are too fuzzy to conclusively answer the latter, but we can certainly speculate. The bacteria we identified as harboring these ancient sulfa drug resistance genes are all soil and freshwater bacteria that thrive under the well-irrigated subsoil of farms. And farmers have been adding huge amounts of sulfa drugs to animal feed for the past 50 years.

The sublethal concentrations of sulfa drugs in the soil are the perfect setting for resistance genes to be transferred from these ancient resistant bacterial populations to other bacteria. All it takes is for one lucky bacterium to meet one of these ancient resistant ones in the subsoil. They trade some genes, one bacterium to the next, and resistance spreads until a newly minted resistant bacterium eventually makes it to the groundwater supply you drink from. You do the math.

Nothing new under the sun

As for why sulfa drug resistance genes would be around 500 million years ago, there are two plausible explanations. On the one hand, it could be that 500 million years ago there was a bacterium that synthesized sulfa drugs, which would explain the evolution of resistance. However, the lack of remnants from such a biosynthetic pathway makes this unlikely.

On the other hand, resistant bacteria may have been around just by chance. The argument here is that there are so many bacteria, and such diversity, that chances are that some of them are going to be resistant to anything scientists come up with. This is a sobering thought.

Then again, this is already the baseline for antibiotics. Like climate change, antibiotic resistance is one of those problems that always seem to be a couple decades away. And it may well be. A turning point for me in the climate change debate was a decade-old opinion piece in New Scientist. It stated that we should make every possible effort to prevent climate change, especially in the unlikely case that it was not caused by man, because that would mean that all we can do is palliate a natural phenomenon.

Our research points in the same direction. If resistance is already out there, drug development can offer only temporary relief. The challenge then is not to quell resistance, but to avoid its spread. It is a big challenge, but not an insurmountable one. Not feeding wonder drugs to pigs would do nicely, for starters.The Conversation

Ivan Erill, Associate Professor of Biological Sciences, University of Maryland, Baltimore County

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Doctors may be prescribing antibiotics for longer than needed



File 20190304 110130 13uen4a.jpg?ixlib=rb 1.1
Most recommended courses last between three and seven days.
Shutterstock

Allen Cheng, Monash University

For most infections, the long-standing advice is to take a full course of antibiotics.

The rationale for not simply stopping antibiotics as soon as you start to feel better is that antibiotics don’t kill the bacteria instantly. If stopped too early, the remaining bacteria, which are exposed to low concentrations of antibiotics, tend to be more resistant. These can then re-grow, causing recurrent infection, or spread to other people.

The recommended length of the course depends on the type of infection, the likely cause, and how effective the antibiotics are at killing the bacterium and penetrating to the site of infection.

For infections commonly seen in general practice, most recommended courses last between three and seven days. For more serious infections requiring hospitalisation, the recommendations are generally a little longer.




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A recent study from the United Kingdom found a substantial proportion of antibiotic prescriptions in general practice were for longer than these recommendations. While for each prescription this may have only been a few days longer, for the UK as a whole this amounted to about 1.3 million days of antibiotics more that would have been necessary.

Researchers are currently investigating how much of a problem this is in Australia.

There’s little evidence to suggest longer courses of antibiotics benefit patients. In fact, even the recommended lengths could be too long for many infections.

Why are courses longer than recommended?

The most important determinant of duration in primary care is probably the size of the pack the antibiotics come in.

But the number of tablets in a pack is rarely the same as the length of a course. One Australian study looked at 32 common prescribing scenarios and found that the pack size only matched the recommended duration of antibiotics in four cases.

Other reasons antibiotics may be prescribed for longer than recommended is when patients are given “repeats” and taking a second course of antibiotics. Often, the doctor isn’t actively prescribing a second course, but their medical prescribing software is printing a “repeat” on their prescription by default.




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In hospitals, clinical uncertainty plays a large role. It is sometimes suggested that antibiotics are used for the benefit of the patient, but at other times to allay the treating doctor’s anxiety.

While the motivation to make sure infections are properly treated is understandable and well-intentioned, particularly in patients who might still be critically unwell for other reasons, continuing antibiotics for too long increases the risk of side effects and antibiotic resistance.

Do we even need a full course?

We may be able to stop antibiotics before we reach the end of our course. The body has the capacity of “mop up” small numbers of bacteria, so at least for milder infections, it may not be necessary to kill them all.

This is important because using antibiotics for too long can be a problem in causing antibiotic resistance. This can occur within individual patients by exposing bacteria elsewhere in the body to antibiotics, but also because antibiotics are eliminated from the body and can contaminate the environment.

We didn’t always standardise the duration of antibiotics. Harry Dowling, one of the pioneers of early antibiotic use, once said

The duration of treatment just evolved. There was no rationale for any single length of time. We saw how long it took for the temperature to come down and gave antibiotics until it did, and then some.

The durations recommended in guidelines often come from arbitrary decisions made in early studies, which have translated into some odd “rules” about antibiotics:

  • prime numbers for durations of up to a week (three, five or seven days)
  • even numbers for more serious infections that take weeks to eradicate (two, four or six weeks)
  • multiples of three for really tenacious infections such as bone infections (three months) or TB (six months).

In writing guidelines for doctors, we often wrestle with whether to set a fixed duration (such as seven days), a range (five to ten days), a minimum (at least five days), a maximum (up to ten days) or wordy qualifications (usually five days, or ten days for severe illness or where there is a slow response).




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What about serious infections?

For deep or severe infections, we want to be sure the infection won’t return. Recent research has focused on defining the shortest effective duration of treatments.

A recent trial compared whether seven days or 14 days of antibiotics were required for some types of bloodstream infection, and found outcomes to be similar.

Researchers have also been testing the use of oral antibiotics for two of the most difficult infections to treat – endocarditis (infection of the heart valves) and ostemyelitis (infection of bone) – which have needed intravenous antibiotics for six weeks or longer. These trials have shown a shorter course of intravenous antibiotics with an early switch to oral antibiotics may be adequate.

Shortening the duration of antibiotics is one important way to reduce antibiotic use, the key driver of antibiotic resistance.




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The Conversation


Allen Cheng, Professor in Infectious Diseases Epidemiology, Monash University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Health Check: should you take probiotics when you’re on antibiotics?



File 20181112 83596 15uhq79.jpg?ixlib=rb 1.1
We still don’t know what types of bacteria are truly beneficial.
Andry Jeymsss/Shutterstock

Lito Papanicolas, South Australian Health & Medical Research Institute and Geraint Rogers, South Australian Health & Medical Research Institute

If you take antibiotics, there’s a good chance you’ll also get diarrhoea.

Antibiotics kill harmful bacteria that cause disease. But they also cause collateral damage to the microbiome, the complex community of bacteria that live in our gut. This results in a profound, though usually temporary, depletion of the beneficial bacteria.

One popular strategy to mitigate the disruption is to take a probiotic supplement containing live bacteria during, or following, a course of antibiotics.




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The logic is simple: beneficial bacterial in the gut are damaged by antibiotics. So why not replace them with the “beneficial” bacterial strains in probiotics to assist gut bacteria returning to a “balanced” state?

But the answer is more complicated.

There is currently some evidence that taking probiotics can prevent antibiotic-associated diarrhoea. This effect is relatively small, with 13 people needing to take probiotics for one episode of diarrhoea to be averted.

But these studies have often neglected to evaluate potential harms of probiotic use and haven’t looked at their impact on the wider gut microbiome.

Pros and cons of probiotics

The assumption that there is little downside to taking probiotics was challenged in a recent Israeli study.

The participants were given antibiotics and split into two groups: the first group was given an 11-strain probiotic preparation for four weeks; the second was given a placebo, or dummy pill.

The researchers found the antibiotic damage to the gut bacteria of those in the first group allowed the probiotic strains to effectively colonise the gut. But this colonisation delayed the normal recovery of the microbiota, which remained perturbed for the entire six month study period.

In contrast, the microbiota of the second group returned to normal within three weeks of finishing antibiotics.




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Health Check: should healthy people take probiotic supplements?


This research exposes a perhaps unexpected truth: we still don’t know what types of bacteria are truly beneficial or even what constitutes a healthy microbiome.

The answer is unlikely to be that individual bacterial strains are particularly helpful.

It’s more likely a diverse community of thousands of different types of microbes working together can provide health benefits. This microbial community is as individual as each one of us, meaning there is not just one configuration that will result in health or illness.

So, it’s unlikely that the addition of one or even 11 strains of bacteria in a probiotic could somehow balance this complex system.

A more effective (but less palatable) alternative?

The Israeli study also explored an alternative approach to microbiome restoration.

One group of participants had their own stool collected and frozen prior to antibiotic treatment. It was then re-instilled into their gut at the end of the antibiotic therapy.

This treatment, known as autologous faecal transplantation, was able to restore the microbiome to original levels after just eight days. The other group took 21 days to recover.




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This approach has also been shown to effectively restore the gut microbiome following combined antibiotic and chemotherapy treatment. These patients are predictably at risk of serious complications, such as bloodstream infection, as a result of microbiome disruption.

Research currently underway will help us understand whether microbiome restoration with autologous faecal transplantation will translate into tangible benefits for these patients.

But such an approach would not be a realistic option for most people.

Feed the good bacteria

Good food for gut bacteria.
Roosa Kulju

A more practical strategy to aid recovery is to provide the good bacteria in your gut with their preferred source of nutrition: fibre. Fibrous compounds pass undigested through the small intestine and into the colon, where they act as fuel for bacterial fermentation.

So if you’re taking antibiotics or have recently finished a course, make sure you eat plenty of vegetables, fruit and wholegrains. Your gut bacteria will thank you for it.The Conversation

Lito Papanicolas, Infectious diseases specialist and PhD candidate, South Australian Health & Medical Research Institute and Geraint Rogers, Professor; Director, Microbiome Research, South Australian Health & Medical Research Institute

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Egyptian Couple Shot by Muslim Extremists Undaunted in Ministry


Left for dead, Christians offer to drop charges if allowed to construct church building.

CAIRO, Egypt, June 9 (CDN) — Rasha Samir was sure her husband, Ephraim Shehata, was dead.

He was covered with blood, had two bullets inside him and was lying facedown in the dust of a dirt road. Samir was lying on top of him doing her best to shelter him from the onslaught of approaching gunmen.

With arms outstretched, the men surrounded Samir and Shehata and pumped off round after round at the couple. Seconds before, Samir could hear her husband mumbling Bible verses. But one bullet had pierced his neck, and now he wasn’t moving. In a blind terror, Samir tried desperately to stop her panicked breathing and convincingly lie still, hoping the gunmen would go away.

Finally, the gunfire stopped and one of the men spoke. “Let’s go. They’re dead.”

 

‘Break the Hearts’

On the afternoon of Feb. 27, lay pastor Shehata and his wife Samir were ambushed on a desolate street by a group of Islamic gunmen outside the village of Teleda in Upper Egypt.

The attack was meant to “break the hearts of the Christians” in the area, Samir said.

The attackers shot Shehata twice, once in the stomach through the back, and once in the neck. They shot Samir in the arm. Both survived the attack, but Shehata is still in the midst of a difficult recovery. The shooters have since been arrested and are in jail awaiting trial. A trial cannot begin until Shehata has recovered enough to attend court proceedings.

Despite this trauma, being left with debilitating injuries, more than 85,000 Egyptian pounds (US$14,855) in medical bills and possible long-term unemployment, Shehata is willing to drop all criminal charges against his attackers – and avoid what could be a very embarrassing trial for the nation – if the government will stop blocking Shehata from constructing a church building.

Before Shehata was shot, one of the attackers pushed him off his motorcycle and told him he was going to teach him a lesson about “running around” or being an active Christian.

Because of his ministry, the 34-year-old Shehata, a Coptic Orthodox Christian, was arguably the most visible Christian in his community. When he wasn’t working as a lab technician or attending legal classes at a local college, he was going door-to-door among Christians to encourage them in any way he could. He also ran a community center and medical clinic out of a converted two-bedroom apartment. His main goal, he said, was to “help Christians be strong in their faith.”

The center, open now for five years, provided much-needed basic medical services for surrounding residents for free, irrespective of their religion. The center also provided sewing training and a worksite for Christian women so they could gain extra income. Before the center was open in its present location, he ran similar services out of a relative’s apartment.

“We teach them something that can help them with the future, and when they get married they can have some way to work and it will help them get money for their families,” Shehata said.

Additionally, the center was used to teach hygiene and sanitation basics to area residents, a vital service to a community that uses well water that is often polluted or full of diseases. Along with these services, Shehata and his wife ran several development projects, repairing the roofs of shelters for poor people, installing plumbing, toilets and electrical systems. The center also distributed free food to the elderly and the infirm.

The center has been run by donations and nominal fees used to pay the rent for the apartment. Shehata has continued to run the programs as aggressively as he can, but he said that even before the shooting that the center was barely scraping by.

“We have no money to build or improve anything,” he said. “We have a safe, but no money to put in it.”

 

Tense Atmosphere

In the weeks before the shooting, Teleda and the surrounding villages were gripped with fear.

Christians in the community had been receiving death threats by phone after a Muslim man died during an attack on a Christian couple. On Feb. 2, a group of men in nearby Samalout tried to abduct a Coptic woman from a three-wheeled motorcycle her husband was driving. The husband, Zarif Elia, punched one of the attackers in the nose. The Muslim, Basem Abul-Eid, dropped dead on the spot.

Elia was arrested and charged with murder. An autopsy later revealed that the man died of a heart attack, but local Muslims were incensed.

Already in the spotlight for his ministry activities, Shehata heightened his profile when he warned government officials that Christians were going to be attacked, as they had been in Farshout and Nag Hammadi the previous month. He also gave an interview to a human rights activist that was posted on numerous Coptic websites. Because of this, government troops were deployed to the town, and extremists were unable to take revenge on local Christians – but only after almost the
entire Christian community was placed under house arrest.

“They chose me,” Shehata said, “Because they thought I was the one serving everybody, and I was the one who wrote the government telling them that Muslims were going to set fire to the Christian houses because of the death.”

Because of his busy schedule, Shehata and Samir, 27, were only able to spend Fridays and part of every Saturday together in a village in Samalut, where Shehata lives. Every Saturday after seeing Samir, Shehata would drive her back through Teleda to the village where she lives, close to her family. Samalut is a town approximately 105 kilometers (65 miles) south of Cairo.

On the afternoon of Feb. 27, Shehata and his wife were on a motorcycle on a desolate stretch of hard-packed dirt road. Other than a few scattered farming structures, there was nothing near the road but the Nile River on one side, and open fields dotted with palm trees on the other.

Shehata approached a torn-up section of the road and slowed down. A man walked up to the vehicle carrying a big wooden stick and forced him to stop. Shehata asked the man what was wrong, but he only pushed Shehata off the motorcycle and told him, “I’m going to stop you from running around,” Samir recounted.

Shehata asked the man to let Samir go. “Whatever you are going to do, do it to me,” he told the man.

The man didn’t listen and began hitting Shehata on the leg with the stick. As Shehata stumbled, Samir screamed for the man to leave them alone. The man lifted the stick again, clubbed Shehata once more on the leg and knocked him to the ground. As Shehata struggled to get up, the man took out a pistol, leveled it at Shehata’s back and squeezed the trigger.

Samir started praying and screaming Jesus’ name. The man turned toward her, raised the pistol once more, squeezed off another round, and shot Samir in the arm. Samir looked around and saw a few men running toward her, but her heart sank when she realized they had come not to help them but to join the assault.

Samir jumped on top of Shehata, rolled on to her back and started begging her attackers for their lives, but the men, now four in all, kept firing. Bullets were flying everywhere.

“I was scared. I thought I was going to die and that the angels were going to come and get our spirits,” Samir said. “I started praying, ‘Please God, forgive me, I’m a sinner and I am going to die.’”

Samir decided to play dead. She leaned back toward her husband, closed her eyes, went limp and tried to stop breathing. She said she felt that Shehata was dying underneath her.

“I could hear him saying some of the Scriptures, the one about the righteous thief [saying] ‘Remember me when you enter Paradise,’” she said. “Then a bullet went through his neck, and he stopped saying anything.”

Samir has no way of knowing how much time passed, but eventually the firing stopped. After she heard one of the shooters say, “Let’s go, they’re dead,” moments later she opened her eyes and the men were gone. When she lifted her head, she heard her husband moan.

 

Unlikely Survival

When Shehata arrived at the hospital, his doctors didn’t think he would survive. He had lost a tremendous amount of blood, a bullet had split his kidney in two, and the other bullet was lodged in his neck, leaving him partially paralyzed.

His heartbeat was so faint it couldn’t be detected. He was also riddled with a seemingly limitless supply of bullet fragments throughout his body.

Samir, though seriously injured, had fared much better than Shehata. The bullet went into her arm but otherwise left her uninjured. When she was shot, Samir was wearing a maternity coat. She wasn’t pregnant, but the couple had bought the coat in hopes she soon would be. Samir said she thinks the gunman who shot her thought he had hit her body, instead of just her arm.

The church leadership in Samalut was quickly informed about the shooting and summoned the best doctors they could, who quickly traveled to help Shehata and Samir. By chance, the hospital had a large supply of blood matching Shehata’s blood type because of an elective surgical procedure that was cancelled. The bullets were removed, and his kidney was repaired. The doctors however, were forced to leave many of the bullet fragments in Shehata’s body.

As difficult as it was to piece Shehata’s broken body back together, it paled in comparison with the recovery he had to suffer through. He endured multiple surgeries and was near death several times during his 70 days of hospitalization.

Early on, Shehata was struck with a massive infection. Also, because part of his internal tissue was cut off from its blood supply, it literally started to rot inside him. He began to swell and was in agony.

“I was screaming, and they brought the doctors,” Shehata said. The doctors decided to operate immediately.

When a surgeon removed one of the clamps holding Shehata’s abdomen together, the intense pressure popped off most of the other clamps. Surgeons removed some stomach tissue, part of his colon and more than a liter of infectious liquid.

Shehata could not eat normally and lost 35 kilograms (approximately 77 lbs.). He also couldn’t evacuate his bowels for at least 11 days, his wife said.

Despite the doctors’ best efforts, infections continued to rage through Shehata’s body, accompanied by alarming spikes in body temperature.

Eventually, doctors sent him to a hospital in Cairo, where he spent a week under treatment. A doctor there prescribed a different regimen of antibiotics that successfully fought the infection and returned Shehata’s body temperature to normal.

Shehata is recovering at home now, but he still has a host of medical problems. He has to take a massive amount of painkillers and is essentially bedridden. He cannot walk without assistance, is unable to move the fingers on his left hand and cannot eat solid food. In approximately two months he will undergo yet another surgery that, if all goes well, will allow him to use the bathroom normally.

“Even now I can’t walk properly, and I can’t lift my leg more than 10 or 20 centimeters. I need someone to help me just to pull up my underwear,” Shehata said. “I can move my arm, but I can’t move my fingers.”

Samir does not complain about her condition or that of Shehata. Instead, she sees the fact that she and her husband are even alive as a testament to God’s faithfulness. She said she thinks God allowed them to be struck with the bullets that injured them but pushed away the bullets that would have killed them.

“There were lots of bullets being shot, but they didn’t hit us, only three or four,” she said. “Where are the others?”

Even in the brutal process of recovery, Samir found cause for thanks. In the beginning, Shehata couldn’t move his left arm, but now he can. “Thank God and thank Jesus, it was His blessing to us,” Samir said. “We were kind of dead, now we are alive."

Still, Samir admits that sometimes her faith waivers. She is facing the possibility that Shehata might not work for some time, if ever. The couple owes the 85,000 Egyptian pounds (US$14,855) in medical bills, and continuing their ministry at the center and in the surrounding villages will be difficult at best.

“I am scared now, more so than during the shooting,” she said. “Ephraim said do not be afraid, it is supposed to make us stronger.”

So Samir prays for strength for her husband to heal and for patience. In the meantime, she said she looks forward to the day when the struggles from the shooting are over and she can look back and see how God used it to shape them.

“There is a great work the Lord is doing in our lives, we may not know what the reason is now, but maybe some day we will,” Samir said.

 

Government Opposition

For the past 10 years, Shehata has tried to erect a church building, or at a minimum a house, that he could use as a dedicated community center. But local Muslims and Egypt’s State Security Investigations (SSI) agency have blocked him every step of the way. He had, until the shooting happened, all but given up on constructing the church building.

On numerous occasions, Shehata has been stopped from holding group prayer meetings after people complained to the SSI. In one incident, a man paid by a land owner to watch a piece of property near the community center complained to the SSI that Shehata was holding prayer meetings at the facility. The SSI made Shehata sign papers stating he wouldn’t hold prayer meetings at the center.

At one time, Shehata had hoped to build a house to use as a community center on property that had been given to him for that purpose. Residents spread a rumor that he was actually erecting a church building, and police massed at the property to prevent him from doing any construction.

There is no church in the town where Shehata lives or in the surrounding villages. Shehata admits he would like to put up a church building on the donated property but says it is impossible, so he doesn’t even try.

In Egypt constructing or even repairing a church building can only be done after a complex government approval process. In effect, it makes it impossible to build a place for Christian worship. By comparison, the construction of mosques is encouraged through a system of subsidies.

“It is not allowed to build a church in Egypt,” Shehata said. “We can’t build a house. We can’t build a community center. And we can’t build a church.”

Because of this, Shehata and his wife organize transportation from surrounding villages to St. Mark’s Cathedral in Samalut for Friday services and sacraments. Because of the lack of transportation options, the congregants are forced to ride in a dozen open-top cattle cars.

“We take them not in proper cars or micro-buses, but trucks – the same trucks we use to move animals,” he said.

The trip is dangerous. A year ago a man fell out of one of the trucks onto the road and died. Shehata said bluntly that Christians are dying in Egypt because the government won’t allow them to construct church buildings.

“I feel upset about the man who died on the way going to church,” he said.

 

Church-for-Charges Swap

The shooters who attacked Shehata and Samir are in jail awaiting trial. The couple has identified each of the men, but even if they hadn’t, finding them for arrest was not a difficult task. The village the attackers came from erupted in celebration when they heard the pastor and his wife were dead.

Shehata now sees the shooting as a horrible incident that can be turned to the good of the believers he serves. He said he finds it particularly frustrating that numerous mosques have sprouted up in his community and surrounding areas during the 10 years he has been prevented from putting up a church building, or even a house. There are two mosques alone on the street of the man who died while being trucked to church services, he said.

Shehata has decided to forgo justice in pursuit of an opportunity to finally construct a church building. He has approached the SSI through church leaders, saying that if he is allowed to construct a church building, then he will take no part in the criminal prosecution of the shooters.

“I have told the security forces through the priests that I will drop the case if they can let us build the church on the piece of land,” he said.

The proposal isn’t without possibilities. His trial has the potential of being internationally embarrassing. It raises questions about fairness in Egyptian society during an upcoming presidential election that will be watched by the world.

Regardless of what happens, Shehata said all he wants is peace and for the rights of Christians to be respected. He said that in Egypt, Christians have less value than the “birds of the air” mentioned in the Bible. According to Luke 12:6, five sparrows sold for two pennies in ancient times.

“We are not to be killed like birds, slaughtered,” he said. “We are human.”

Report from Compass Direct News