The first time Naowarat Cheeptham ventured down into the Iron Curtain Cave, one day in 2011, the darkness was all-consuming. Turning away from the steel ladder – the only route back to the small square of sunlight far overhead – the biologist forced herself to continue forward.
Cheeptham, 48, who is known by her friends as Ann, did not stumble upon the Iron Curtain herself. The cave, located in the hills of Chilliwack, in British Columbia, Canada, were discovered in 1993 by Rob Wall, a local construction contractor and amateur caver. Wall was exploring the hills in search of uncharted caverns he might open up and explore for his own pleasure. A great deal of caves in this area of Canada are actually closed sinkholes. As such, Wall’s search involved a process called, unsurprisingly, digging, in which promising, sunken areas of ground are excavated. One day, Wall was walking through the woods and tripped into such a hole. He returned the next day with a friend and a shovel. The pair dug for three hours, uncovering a hole ten metres deep, with two small rooms at the bottom. It was everything Wall had been looking for.
It wasn’t until six months later, in the autumn of 1993, when Wall was showing off his discovery to a group of friends, that one of them noticed a breeze blowing through from the back of the cave. The group investigated, shifting rocks until they opened up an entrance to half a kilometre of pristine caves. The underground network shone with gypsum crystal, the walls and floor bristling with stalagmites and stalactites. Not human being had been there before. “It was beautiful,” Wall says.
Wall was approached by Cheeptham in 2011. The biologist was on the lookout for local caves to explore and Wall invited her to give a presentation to the Chilliwack River Valley Cavers (CRVC), explaining her project. Cheeptham explained that the dark, dank subterranean caves are teeming with life in the form of largely uncharted extremophiles – organisms that thrive in conditions that would be geochemically hostile to most life forms on earth. For Cheeptham and her colleagues from Thompson Rivers University Department of Biological Sciences, spelunking in search of these extremophiles is no mere hobby, but a last-ditch attempt to find a solution to one of the biggest global threats facing humanity today: antibiotic resistance.
While extremophiles are not the only avenue in the search for new antibiotics, their ability to not only survive but thrive in habitats where other bacteria would die suggests their chemical secretions are particularly potent. Caves are a rich source of less-studied bacteria because of their natural biodiversity, and seclusion from other environments in which bacteria usually develop.
It is not actually the bacteria themselves that are used to make antibiotics, but their metabolites – chemical compounds produced by them as a by-product of their growth. Yeast’s metabolite, for example, is the result of fermentation. It was once thought that some of these metabolites existed to kill off competing bacteria. However, new thinking popularised by a number of biologists, including Julian Davies at the University of British Columbia, argues that the true function of such metabolites in nature may be to act as a form of language between bacteria, enabling them to communicate and actually share resources. In a cave, this is particularly vital. After all, as Cheeptham points out, “[In a cave habitat] is it better for them all to compete and die, or to live together in co-operation?”
After watching Cheeptham’s presentation, local caver Doug Storozynski, 51, volunteered to help her explore the local caves. While not as technically challenging as other caves in the vicinity, the Iron Curtain still contains its share of tight squeezes, and requires an experienced guide to navigate safely. When they descended into the gloom, Cheeptham felt, at first, claustrophobic and scared. But as she and her team ventured deeper through cramped crawl spaces, numbing underground waterways and abrasive rock walls, their way lit by head-torches, the cave came alive. Stalactites hung from the ceilings, stalagmites rising from the ancient floor.
Bacteria inhabit secondary mineral deposits in the form of soda-straw speleothems – natural calcium-based deposits which include stalactites and stalagmites. After 15 minutes of feeling their way along in the near-dark, Cheeptham and her team reached the back wall of the cave, where a cascade of red-tinged, curtain-like limescale deposits give the cave its name. Next to this wall, the ceiling sloped down into the darkness of a side recess. It was the 60-centimetre stalagmites hanging from this ceiling that Cheeptham targeted. As the blue-grey caverns took shape, Cheeptham’s trepidation was replaced by curiosity and excitement.
Crawling into position, she knelt in the small space between floor and stalagmite and retrieved the sample kit from her rucksack. With sterile forceps she scraped away a near-minuscule section from the tip of the first stalagmite, dropping it into a 50ml Falcon Tube before securing it away. She worked quickly by the light of her head torch, filling her half-dozen containers with stalagmite samples. The team then retraced their steps back to the surface. Cheeptham deposited the samples in the coolbag designed to keep the bacteria alive until they could be analysed in her lab.
Around the world, everyday surgical procedures, from treatments for common infections to chemotherapy, rely on antibiotics. In the past decade, however, the drugs we rely on to keep us safe from everything from E. coli to severe acute respiratory syndrome (SARS) are failing to keep up with the rapid evolution of such infections and viruses. As these antibiotics continue to lose their efficacy, we lose our ability to treat even the most basic of illnesses. The situation is so severe that the World Health Organization regards antibiotic resistance as “one of the biggest threats to global health, food security and development today”.
Nor is this a new crisis. In 2014, the Prime Minister David Cameron appointed economist Jim O’Neill to investigate the economic fallout of antibiotic resistance. The resulting report, the Review on Antimicrobial Resistance, put the global annual death toll due to drug-resistant superbugs at 700,000, with an estimated annual mortality rate of ten million by 2050. O’Neill also predicted that, should the crisis continue without a satisfactory response, the reduction in worldwide population would diminish the global economic output by up to 3.5 per cent, at a cost of $100 trillion (£63tn) – roughly 35 times the GDP of the UK. Four years later, we’re no closer to solving the problem.
As of April 2018, a new strain of typhoid – resistant to five different antibiotics – has killed four people in Pakistan and affecting the health of more than 800 others. Also this year, Public Health England reported the “worst ever” case of Neisseria gonorrhoeae, after UK instances of the infection rocketed from just under 15,000 in 2008 to 41,000 in 2015. Even the antibiotic colistin – often administered as the final treatment when all other antibiotics have failed – is losing its effectiveness. A 2017 summit of the American Society for Microbiology reported that bacteria possessing the colistin-resistant mcr-1 gene has now spread around the world. In April 2018, in response to this dire prognosis, Rumina Hasan, a pathology professor at Pakistan’s Aga Khan University, told The New York Times that “Antibiotic resistance is a threat to all of modern medicine — and the scary part is, we’re out of options.”
Contrary to common misconception, human beings have not developed a resistance to antibiotics through overexposure. Instead, the bacteria themselves have evolved to evade our methods of killing them. We have, according to Cheeptham, around 1.3 kilograms of bacteria in and on our bodies at any one time. Their mass is roughly the equivalent to that of the human brain and, despite what domestic kitchen cleaners and soaps would have you believe, 99.9 per cent of all bacteria are actually neutral or beneficial to our health.
“Previously, we thought that overuse and misuse of commercially available antibiotics caused resistance in bacteria,” Cheeptham explains. “But the truth is that we train them. When bacteria see triclosan [an antibacterial agent found in cleaning products, soap and toothpaste] coming towards them, they want to live, like all life on Earth. Most will die, but some figure out defence mechanisms that help them survive, such as creating a pore in their cell wall to allow them to pump out the drug faster than it comes in.” She taps her finger on the table to emphasis a point that she is clearly still in awe of. “Bacteria are smarter than us.”
This isn’t the only revelation that has changed the way researchers look at bacteria. “We’ve known since 1928 that bacteria produce both asexually and sexually, but we didn’t really make the connection between the latter method – also known as ‘horizontal gene transfer’ – and the passing on of antibiotic-resistant genes until very recently,” Cheeptham explains.
Most typically, bacteria produce offspring asexually by dividing their cells, creating an exact copy of the genome (known as vertical gene transfer). In this way, antibiotics are able to kill harmful bacteria as they’re dealing with an exact genetic replica of the harmful organism each time. However, during sexual reproduction, genes are exchanged between parent cells, and the offspring retains both sets of genes, creating a more complex organism. This can happen both within a species, and between species. Not all forms of E. coli, for example, are harmful. But there’s nothing to stop virulent strains of E. coli bacteria (such as O157:H7, or O104:H4) mixing with salmonella to create something altogether more lethal, and more difficult to kill.
To further complicate matters, most of the antibiotics we currently employ are considered "broad spectrum" drugs. Essentially, they’re engineered to kill all bacteria they come into contact with, whether good, bad or neutral. They are not specialised to deal with specific infections, let alone their mutated cousins. By wiping out our beneficial bacteria, these broad-spectrum antibiotics lower our immune system. And when our defences are down, new strains of antibiotic-resistant, and potentially fatal, superbugs can take hold. In short, when it comes to modern antibiotics, the standard medical procedure is to employ napalm when we really require a sniper.
Cheeptham is part of a growing coterie of scientists who believes an intelligent – if complex – solution exists. As of 2016, biologists at Indiana University estimated that 99.9999 per cent of all microbial species – some one trillion different species, whose natural chemical secretions form the base of all antibiotics – are still to be discovered. And Cheeptham believes that Canada’s Iron Curtain Cave – so called because of its bountiful iron deposits – represents one of our best chances at locating these new bacteria and using them to develop new antibiotics.
To Cheeptham, the search for the perfect cave has been a long journey. Born in Nakhon Sawan, Thailand, in 1970, to primary-school teachers, she credits her father for her interest in biology. “He graduated with a B.Sc. in Biology when I was 11,” she explains. “He took me to collect samples, and I became obsessed.”
Later, in 1992, after completing her own undergraduate degree in microbiology and biochemistry at Chang Mai University in northern Thailand, she began working alongside Fusao Tomita, previously head of research and development at Kyowa Hakko – at that time the third-largest pharmaceutical company in Japan. Under Tomita’s tutelage, Cheeptham’s focused her master's and PhD research on the possibility of developing new antifungal agents from fungi.
After finishing her PhD, she returned to Thailand in 1999 to continue her work at Chang Mai University. An article on cave bacteria by Diana Northup, an expert in geomicrobiology and biology at the University of New Mexico, convinced Cheeptham to make the switch to extremophiles. “I thought that if I went into a more extreme environment I would have a better chance of finding something new,” she explains.
Cheeptham‘s search for extremophiles initially took her to Thailand’s southern mangrove swamps, but she had a hunch that she would have better luck searching caves. The only issue was that the majority of accessible Thai caves have been opened up to tourists and outfitted with cement floors, artificial lamps and Buddha statues – not to mention scores of people trekking in and out each week. In other words, the antithesis of the pristine environments in which rare and unique bacteria are wont to develop. Along with her husband, Joe Dobson, Cheeptham made the move to his native British Columbia in 2001 and set up at Thompson Rivers the following year.
Ten years later, she discovered what she hopes to be the perfect cave. In their 2016 paper outlining their initial findings, (published in the journal Diversity) Cheeptham and her colleagues reported cataloguing 100 bacteria isolates in the Iron Curtain Cave. Of these, 12.3 per cent were unknown, and may even be completely new bacteria. So far, two of them have proved to be efficient against multi-drug-resistant microbial strains.
It’s early spring and I’m in the passenger seat of a truck as Rob Wall drives us through the remote backroads of the Chilliwack Basin, en route to the cave. Endless wooded hills stretch by on either side, and it is easy to imagine the grand network of underground systems hidden beneath the depths of the forest.
There, in the midst of a forest teeming with life, is a metre-wide metal door on the side of a mossy mound, like some kind of steampunk Hobbit hole. Wall and Storozynski are the only people able to provide access. Once the gate is open you will descend ten metres (down a pair of ladders laid end to end) into the bowels of the earth. There you’ll find half a kilometre of winding limestone tunnels, subterranean pools and claustrophobic crevices, stalagmites hanging from the ceilings, lords of the darkness.
As a member of the CRVC, Wall – now in his forties – acts as custodian of the Iron Curtain Cave, working with the government to control access. Its exact location is kept secret after other caves in the area were vandalised by weekend partygoers – an ongoing problem, to Wall’s immense chagrin. Protecting this unique resource is key; a pair of metal gates protect the cave from the world above, and rigorous sterilisation procedures must be followed to prevent caving gear and scientific instruments from tainting the isolated bacteria.
Decontaminated or completely new caving equipment is required if the wearer has acessed another cave the same day. This is in order to prevent cross-contamination of organic matter, which may in turn destabilise a cave’s particular habitat, potentially destroying its unique – and possibly useful – bacteria population. Often, disposable Tyvek Coveralls are worn, then sealed in a plastic bag and sprayed with disinfectant upon exiting the cave. Easy-clean boots with rubber soles are preferred, and footwear must be changed before entering, and upon exiting, any cave. Naturally, scientific materials used in the collection of samples must either be sterilised, or previously unused and kept sealed in their packaging until required.
Storozynski takes point as he leads us into the depths. It is his job to ensure the safety of both Cheeptham and her team – and the cave environment – on their sample-collecting trips into the cave. While not as technically challenging as other caves in the vicinity, the Iron Curtain Cave has its share of tight squeezes, and requires an experienced guide to navigate safely.
Storozynski and Wall aren’t the only cavers putting their lives at risk in the hunt for new bacteria; a number of cavers from the British Columbia Speleological Federation (BCSF) – the umbrella organisation for caving groups in the province – have ventured into underground vaults across the province to collect samples for Cheeptham. One cave is in grizzly-bear country so requires cavers to helicopter in to avoid attack. Another is only assessible if cavers scuba-dive in, then swim upwards into the cave – a technical feat beyond the abilities of most microbiologists. Without the vital work of these unpaid chaperones, Cheeptham’s research would stop dead in its tracks while the problem of antibiotic resistance continued to grow unimpeded.
During our time below ground, Storozynski leads us beneath low features and through tight crawl spaces, and is careful that we do not disturb the pristine cave walls by brushing against them. He is also tasked with maintaining the strips of luminous tape that guide us through the cave. Stray too far from the path and not only do you risk damaging the cave, you put yourself at serious risk, too; towards the back of the cave a large, metre-wide hole on the edge of the taped-out path leads down into seemingly bottomless blackness. “It goes on forever,” Storozynski says, perhaps only half-joking.
At one point, making room for our team, Storozynski backs up against the cave wall, dislodging a loose rock the size of a fist, which falls against his back. Although uninjured, protocol demands that he warn us of the danger, and his intention to move away from the wall. He does so quickly and the rock falls harmlessly to the floor. A second of baited breath follows. Thankfully, the cave roof remains intact.
Around 250 kilometres north-east of Chilliwack, through logging country, over mountain passes warning of the need for snow chains, and semi-arid grassland ringed by distant mountains, lies the university city of Kamloops. It is here, in a small, L-shaped laboratory on the third floor of Thompson Rivers University’s Science Building, that Cheeptham has had her base of operations since 2002.
Cheeptham’s lab is adorned with blown-up black-and-white photographs of cave bacteria, resembling clusters of grey pinheads on chalk. Along one wall sits a stainless-steel biosafety cabinet, where potentially harmful cave samples are processed. Air pressure, oxygen content, light and mineral availability all force the bacteria to adapt, but it is believed that the intrusion of calcium’s positively charged ions between bacteria DNA strands may cause the biggest change, forcing the bacteria to adapt at a genetic level, or die. Hence why Cheeptham has narrowed her research to crystalline soda straw speleothems, made from deposits of calcium carbonate, or calcium sulphate.
Samples are obtained in the caves using forceps or cotton swabs, then transported to the lab in containment vessels containing agar, and kept at 12 °C, to mimic cave conditions to help keep the microorganisms alive. Assisted by undergraduate students Richenda McFarlane and Keegan Koning, Cheeptham then works to isolate bacteria from cave samples before attempting to cultivate these bacteria on isolation media – the first step in a long and far from certain process.
But, for subterranean bacteria to thrive in the lab, the conditions in which it has developed must be replicated in vitro. This, in Cheeptham’s words, is "a shot in the dark”.
“We don’t know what type of media each bacterium would like to grow on,” Cheeptham admits. “I have to guess what kind of biological, physical and chemical factors they like, then try to mimic that in the lab. It’s never 100 per cent, and we miss a lot of things a lot of the time.”
Even if this nutrient soup proves sufficient to nurture life, there is a long wait in store. Typically, some cave bacteria can take anywhere between two and eight weeks to grow in the lab. To put that into perspective, E. coli doubles its population every 20 minutes or so. Encouraging cave bacteria to grow faster by providing an abundance of nutrients doesn’t work, either. Cheeptham likens this approach to “putting Walmart on top of them.” After all, in a cave, there is no light and what little organic material they do have is carried either via water that seeps down from above, or other means. Far from hindering their growth, it is these very conditions that make cave bacteria unique.
Should Cheeptham’s team manage to isolate the bacteria, and should its metabolite show promise, its genome must then be sequenced, using gene-mining. However, funding is tight and as a result, Cheeptham’s lab is not equipped to carry out this stage of the process. Instead, it collaborates with the Department of Chemistry and Bimolecular Sciences at the University of Ottawa, 4,300km away. There, biochemistry director Christopher Boddy and his PhD student, Jessica Gosse, search the bacteria for a genetic pattern associated with antibiotics that have been successfully used for medical treatment in the past. Should they find this sequence, they’ll then evaluate the bacteria’s antibiotic activity against a number of pathogens and try to better understand how it works. “One of the great things about the collaboration with Ann is that we have very complementary skill sets,” Boddy explains. “She is a fantastic microbiologist with first-rate skills in cultivating bacteria from the environment. My lab is much more molecular in nature. The role we play in this collaboration is in sequencing the genomes of the bacteria that Ann discovers, and using the information from the genomes to guide our discovery of new antibiotics and antifungal drugs.”
Sadly, for Boddy’s team, the quest to formulate new antibacterial drugs has taken on a personal dimension; last year, Gosse lost a friend to a antibiotic-resistant bacterial infection.
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To date, Cheeptham and her Thompson Rivers team have found 100 new bacteria isolates in the Iron Curtain Cave, but are currently only able to pursue the two most promising options. “It’s politics,” Cheeptham sighs. “I don’t have enough students or funding to take [the bacteria] further. We have to focus on the bacteria that have good killing ability, and are consistent. In other words, every time I grow them they need to produce the useful metabolite.”
Still, while Cheeptham is not yet sure what they might be used for, even two new antibiotics would seem to be a valuable aid in the current crisis. But the process of antibiotic development is far from straightforward. “It could take ten to 25 years to get one antibiotic on the shelf,” Cheeptham says. “Do you think any large pharmaceutical company will fund us? It’s tedious work and it’s a crapshoot. We might find 100 bacteria in the cave, but of these, some might be toxic to certain cells. Some might kill too many things at the same time. Think about the profit-orientated nature of pharmaceutical companies. It could take up to $1 billion to develop a new antibiotic, and the companies will only be able to sell them to each person for seven to ten days per dose. There’s no profit for them in that.”
Despite Cheeptham's concerns, the search for new drugs is far from doomed. Since 2014, innovation foundation Nesta has offered its £8 million Longitude Prize to researchers producing noteworthy work in the fight against antibiotic resistance. So, with Cheeptham’s funding problem, why not award them money?
“We actually have a funding issue ourselves,” explains Daniel Berman, prize lead at Nesta's Challenge Prize Centre. Five million pounds of the prize money comes from private investors. The other £3 million comes from the UK Government’s Innovate UK initiative. As such, prize money is restricted to organisations with a presence in the UK. Were they able to award money globally, Berman predicts another problem, “Funders don’t like long time frames. If you look at the drug pipeline right now, the focus is on helping people who have already identified possible new drugs to get them ready for human trials.”
Berman points to the recommendations of Jim O’Neill, the economist behind the AMR Review. O’Neill advocates a system of "market-entry rewards", in which governments contribute to a prize fund of a “few billion dollars”. This is then awarded to companies who find a new antibiotic which can then be distributed cheaply, instead of the company having to sell a high volume of each antibiotic to turn a profit. But, Berman believes, there are problems inherent in this, too. The widespread availability of new broad-spectrum antibiotics would only lead to the same problems of weakened immune systems being opened up to new superbugs. To combat this, Berman believes new antibiotics should be available via tightly-regulated prescriptions only.
Even in an optimistic world where these conditions are met, there is another reason why developing new antibiotics may only ever be a temporary solution. Extremophiles aside, genetic manipulation of studied bacteria is the only other likely avenue when it comes to developing new antibiotics. It is also our current approach. But it is far from reliable. “From the introduction of penicillin in 1928, to streptomycin in 1943, and daptomycin in the 1980s, bacteria always develops a resistance, often within one or two years,” Cheeptham says. “Any drug we make, history has shown us that bacteria will persist, and prevail.” Today, our antibiotics are slightly adapted versions of the original core antibiotic. This is why, for example, pharmacists talk about penicillin G, K, N, O, V, and so on. The problem is that the trick of tweaking the recipe can only be repeated so many times before it ceases to be effective.
Despite the seemingly insurmountable odds stacked against them, Cheeptham and Boddy are optimistic that somewhere out there they’ll discover a new strain of bacteria that will be able to help us for a while, at least. And when it comes to extremophiles, we’ve only just scratched beneath the surface.
“Any environment is potentially interesting,” says Boddy. “We have research focusing on many distinctive places, from ancient archaeological sites to the ocean. It was only in the last 15 years that we were able to cultivate bacteria from marine environments, and now, as a result, an incredible wealth of new antibiotics and anticancer drugs are in advanced clinical trials.”
Cheeptham still doesn’t know if she’ll find new antibiotics by the time she retires. “As a mum, in my own capable way, I would at least feel that I have done my best to try to fight multi-drug resistant infections for my son, and many generations to come,” she says. Regardless, she remains hopeful that the answer to the global, and growing, antibiotic crisis may well have been under our feet all along.
This article was originally published by WIRED UK
