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ScienceNovember 29, 2021

Why you should care about antimicrobial resistance 

Contributing writer
Three things to know about antibiotics header

As we approach two years since the world was turned upside down by the Covid-19 virus, Siouxsie Wiles and Toby Morris explain a related and very serious threat – antimicrobial resistance. 

Each year in November, the WHO-backed campaign World Antimicrobial Awareness Week aims to make more people aware of the global threat that is antimicrobial resistance and to encourage everyone to use antimicrobials more wisely.

This isn’t a new issue. In fact, it’s almost five years to the day since I first wrote about it for the Spinoff. My piece was part of a week-long Te Pūnaha Matatini-backed campaign called InfectedNZ where I asked lots of experts from all around Aotearoa New Zealand to write about the issue from different perspectives.

Dr Jonathan Skinner, a paediatric cardiologist, wrote about what would happen to children’s heart surgery without effective antibiotics. Dr Anita Muthukaruppan and Professor Andrew Shelling wrote about infectious diseases and infertility. And Tiff Mora wrote about what it’s like living with the superbug MRSA. Her incredible daughter and one of my heroes, Eva, was born with a hole in her diaphragm and has battled MRSA infections many times. So much so that Tiff can smell when the superbug is back. 

In December 2016, a month after InfectedNZ, I started writing my book Antibiotic resistance: the end of modern medicine?, which was published in early 2017 and has just been reprinted. Things haven’t improved much in the intervening years. In fact, I think it’s safe to say the pandemic has just exacerbated the problem. 

What are antimicrobials?

Antimicrobials are chemicals that kill or stop the growth of microbes. They are used to treat and prevent infections in humans, animals and plants. Microbes is the generic term for a multitude of life forms, including bacteria, fungi, parasites and viruses. These all differ in what they are made of, their genetic makeup, and their lifestyles and habitats, so antimicrobials can be divided into different categories depending on what type of microbe they target.

Some antimicrobials work against all microbes, but others are much more specific. Antivirals are compounds that target viruses, by stopping them from being able to enter a host cell or by messing with their ability to replicate their genetic material. Similarly, antifungals target fungi, antiparasitics target parasites, and antibiotics target bacteria. That specificity is why antibiotics are no use at all for viral infections and why the antiparasitic ivermectin hasn’t so far been found to be an effective treatment for Covid-19. 

As an aside, here’s an interesting little fact I recently found out about the word antibiotic. I always thought it was coined by microbiologists in the 1940s during the golden age of antibiotic discovery. But according to American doctor and medical historian Professor Howard Markel, it was an American naval commander called Matthew Fontaine Maury who first used the word in his 1860 book Physical Geography of the Sea and Its Meteorology. He took it from the Greek word biōtikos, which is about the ability to live, and was using it to describe his argument against the existence of extraterrestrial life!

What is antimicrobial resistance?

Antimicrobial resistance is what happens when microbes develop the ability to stop antimicrobials from affecting them. Toby Morris and I have explained before one of the ways this process happens, as it’s how new variants of the Covid-19 virus arise. Unlike us, most microbes replicate their genetic material quite rapidly. Some take just a few minutes to make new copies of themselves. Microbes can also easily reach population sizes in the billions if they have the right growth conditions. That means there are plenty of opportunities for chance mistakes to get made in that replication process and for resistant variants to arise.

These variants then grow quite happily in the presence of the antimicrobial, replacing the microbes that can’t. This happens wherever microbes encounter antimicrobials – in human and veterinary medicine, in agriculture, but also in sewage systems and out in the wider environment. Bacteria have an extra and very worrying trick up their sleeve. They can share the ability to share their resistance between each other on mobile bits of genetic material. Then they don’t even need to be in the presence of the antibiotic – they just need to meet the right kind of resistant microbe! This is called horizontal gene transfer and can happen between completely unrelated bacteria.

Why you should care about antimicrobial resistance

Antimicrobials are used to treat people with infectious diseases. They are also used to prevent infections in people, like those undertaking chemotherapy for cancer, or those who need to have surgery. This is especially true for antibiotics. If we lose these incredible medicines, we don’t just lose the ability to treat infected people, we lose our ability to do the medical treatments that form the basis of modern medicine. Antimicrobial resistance already means some people need to be treated with medicines that are less effective, more expensive, more inconvenient, and have more side effects. Some bacteria are now almost untreatable. This impacts all of us, even if you are someone who has never needed to take antibiotics before.

What can we do about antimicrobial resistance?

Antimicrobial resistance is a big problem that is hard to solve. Like the pandemic and climate change, it requires coordinated global effort. And just like the pandemic and climate change, that global action is missing in action. The World Health Organisation released its first report on the issue in 2014, with the organisation’s director-general Dr Margaret Chang saying antimicrobial resistance could bring about “the end of modern medicine”. In July 2014, the UK prime minister, David Cameron, commissioned economist Sir Jim O’Neill to investigate the problem and propose concrete actions to tackle it internationally. The final report and recommendations were released in 2016. We also knew long before the pandemic that making healthcare and the development and delivery of medicines and vaccines a for-profit industry would be disastrous for global health and wellbeing. The pandemic has shown just how true this is. None of us are safe until we are all safe. 

This year I’ve been one of the many people working with Dame Juliet Gerrard, the chief science adviser to the prime minister, and her office this year on a major project looking at the issue of antimicrobial resistance and its relevance for Aotearoa New Zealand. We’ll soon be reporting back with a whole bunch of recommendations on how to tackle it, so keep an eye out for that. 

More Reading

But for now, here are a few concrete things you can do that will help. Don’t demand antibiotics for you or your animals when you or they are unwell. So many antibiotics are prescribed to people who simply don’t need them because they have a viral infection. So, if your doctor or vet says no, don’t pressure them. If they do prescribe you antibiotics, ask them if they are following the most up-to-date prescribing guidelines. These guidelines change all the time, and it can be hard to keep up to date with the changes, so a gentle inquiry could prompt your doctor or vet to check. 

Another problem is the use of similar antimicrobials in human medicine and in agriculture, aquaculture and horticulture. If you can afford it, choose food that’s been produced without the use of antibiotics. Also look at what products you use in your garden. A fungus commonly found in soil has become resistant to the antifungal pesticides used not just in horticulture but in gardening too. Azoles are one of the things to look out for here. Because similar antifungals are used in human medicine, these resistant fungi are now able to cause almost untreatable infections in some vulnerable hospital patients. And these patients can become infected just by being in a bed next to an open window that looks out onto a garden!

Lastly, if, like me, you think you are allergic to penicillin, there is a very high chance you aren’t. Penicillin is a very safe and effective antibiotic and is used to treat all sorts of infections. Around one in 10 of us think we’re allergic to penicillin because we’ve had some sort of reaction to it in the past. The problem with being labelled as penicillin-allergic is that if you do need antibiotics, you’ll have to be given ones that are less effective and may have more side effects. But studies have shown that when most people are retested, they are no longer allergic and can safely take penicillin and related antibiotics. So, if you think you are allergic to penicillin, talk to your doctor or pharmacist to see if you can have your allergy status reviewed. It’ll be better for your health and help our doctors use antibiotics more wisely.

Keep going!
Illustration by Toby Morris, additional design by Tina Tiller
Illustration by Toby Morris, additional design by Tina Tiller

ScienceNovember 26, 2021

Siouxsie Wiles explains the Omicron variant of Covid-19

Contributing writer
Illustration by Toby Morris, additional design by Tina Tiller
Illustration by Toby Morris, additional design by Tina Tiller

All there is to know about the new Covid-19 variant detected in South Africa.

Editor’s note, 27 November: The headline on this article has been updated to reflect the variant’s newly-announced name.

At 8am local time on Thursday, November 25, researchers in South Africa met with government ministers to discuss a new Covid-19 variant they’d detected less than two days before. By 1pm that afternoon the minister of health Dr Joe Phaahia and the director of the Centre for Epidemic Response & Innovation (CERI) professor Tulio de Oliveira were fronting an emergency media briefing to tell the world about B.1.1.529. The World Health Organization’s technical experts will be meeting shortly to decide whether to give B.1.1.529 its own Greek letter. If they follow the current convention, by the time we wake tomorrow, it’s likely “nu” will be the new variant on the block. (Update, 27 November: WHO today announced the variant is to be named Omicron, after the 15th letter in the Greek alphabet. They’ve also added it straight to their Variant of Concern (VOC) list rather than just designated it a Variant of Interest (VOI). It took months for delta to be named a VOC.)

Where’s this new variant come from?

South Africa has recently emerged from its third deadly wave of Covid infections. The most recent wave was caused by the delta variant which had become the dominant strain there just like it has in many other countries. Over the last week or so, cases have begun growing exponentially again in one region in particular. In Gauteng Province, they’ve gone from having a test positivity rate – that’s the number of tests processed that are positive – from under 1% to over 30%. National daily cases have increased from 273 on November 16 to over 1,200 yesterday. Over 80% of those have been in Gauteng Provence and of the cases in Gauteng Province almost all of them now are this new variant.

At first, they thought the spike in cases was being driven by outbreaks at universities and from large gatherings. But with the effective R number jumping from less than 1 to about 2 in a matter of days, both the researchers and the government worried this could be the start of South Africa’s fourth wave.

How did they detect it?

South Africa has the Network for Genomic Surveillance – South Africa, where labs all around the country are sequencing Covid-19 virus samples to look out for any changes in the virus. On Tuesday, November 23, one of the labs in the network identified a new variant that gives a different PCR test result. This was how alpha, the first variant of concern, was identified in the UK.

Like alpha, a deletion in the variant’s genetic material causes a negative S gene PCR result when it should be positive. Because the PCR test looks for more than one gene from the virus, it’s a pattern that allows diagnostic labs to quickly identify the new variant rather than having to rely on whole genome sequencing. If a sample is negative for the S gene but positive for the other genes, then it’s this variant and not delta. It turns out there has been a big increase in recent days in the number of samples testing negative for the S gene. Worryingly, they aren’t just limited to samples coming from people in Gauteng Provence, suggesting the new variant is circulating more widely.

What’s so worrying about the new variant?

The reason they’ve gone public so quickly is to call global attention to what could be the variant to displace delta. Genome sequencing shows this variant contains an unusual constellation of over 50 genome mutations. Check out Toby Morris’s explainer below if you need a reminder of how these mutations arise.

While this variant’s sudden rise could just be due to what’s called the “founder effect” – which is when a mutant takes off not because it is more infectious, but because it is the one that people who are infectious happen to have – the genome sequencing is painting a more worrying picture.

Of its 50 or so mutations, some are already quite well-characterised as being involved in increasing the virus’s transmissibility and ability to evade the immune system. But many of the mutations have not been seen before. This begs the question, how will this combination of mutations impact on each other? Will they make this variant more transmissible than delta? Will the vaccines be less effective against it? Might it reinfect people who’ve already had Covid-19? Will it cause milder or more severe disease?

Researchers in South Africa have already started their experiments to find out, but on the basis of the mutations we do know about, there is real cause for concern. The delta variant has two mutations in its receptor binding domain that help make it more transmissible. This variant has 10. It also has more than 30 mutations in its spike protein. This is the protein all our current vaccines target, so that’s a real worry.

Professor de Oliveira ended the media briefing by saying he hoped he was wrong about this new variant, and it would turn out to not be worse than delta. I hope so too. But if we’ve learned anything this pandemic it’s that rapid action is crucial when it comes to Covid-19. South Africa will need resources to help it control and extinguish this new variant. The world needs to step up or we will all face the consequences.

The fact that this variant has emerged once again highlights how badly the world is handling the pandemic. While here in Aotearoa we are approaching nearly 70% of our total population fully vaccinated, in South Africa that number is less than 25%. They’ve had to start their own mRNA vaccine research and development programme because Pfizer and Moderna won’t increase production to meet the global need or share their technology so others can meet it instead.

Yet again we are reminded that none of us are safe until we are all safe. If you can spare a few dollars, consider making a donation to Unicef who are doing all they can to deliver Covid vaccines to those in need around the world.