On a recent trip, Cliff Kapono hit some of the more popular surf breaks in Ireland, England and Morocco. He is proudly Native Hawaiian and no stranger to the hunt for the perfect wave. But this time he was chasing something even more unusual: microbial swabs from fellow surfers.
Kapono, a 29-year-old biochemist earning his doctorate at the University of California, San Diego, heads up the Surfer Biome Project, a unique effort to determine whether routine exposure to the ocean alters the microbial communities of the body, and whether those alterations might have consequences for surfers – and for the rest of us.
Kapono has collected more than 500 samples by rubbing cotton-tipped swabs over the heads, mouths, navels and other parts of surfers’ bodies, as well as their boards. Volunteers also donate a fecal sample.
He uses mass spectrometry to create high-resolution maps of the chemical metabolites found in each sample.
“We have the ability to see the molecular world, whether it’s bacteria or a fungus or the chemical molecules,” he said.
Then, working in collaboration with UCSD’s Center for Microbiome Innovation – a quick jaunt across the quad from his lab – Kapono and his colleagues sequence and map the microbes found on this unusually amphibious demographic.
He and his colleagues are looking for signs of antibiotic-resistant organisms. Part of their aim is to determine whether, and to what extent, the ocean spreads the genes for resistance.
Many antibiotics used today derive from chemicals produced by microbes to defend themselves or to attack other microorganisms. No surprise, then, that strains of competing bacteria have also evolved the genetic means to shrug off these chemicals.
He and his colleagues are looking for signs of antibiotic-resistant organisms. Part of their aim is to determine whether, and to what extent, the ocean spreads the genes for resistance
While drug resistance comes about because of antibiotic overuse, the genes responsible for creating resistance are widely disseminated in nature and have been evolving in microbes for eons. Startlingly, that means genes giving rise to drug resistance can be found in places untouched by modern antibiotics.
Several years ago, researchers identified antibiotic-resistant genes in a sample of ancient permafrost from Nunavut, in the Canadian Arctic. William Hanage, an epidemiologist at the Harvard School of Public Health, was among those showing that these genes conferred a resistance to amikacin, a semisynthetic drug that did not exist before the 1970s.
“There was a gene that encoded resistance to it in something that was alive 6,000 years ago,” he said in an interview.
Another group led by Hazel Barton, a microbiologist at the University of Akron, discovered microorganisms harboring antibiotic-resistance genes in the Lechuguilla Cave in New Mexico. These bacteria, called Paenibacillus sp. LC231, have been isolated from Earth’s surface for 4 million years, yet testing showed they were capable of fending off 26 of 40 modern antibiotics.
Sixty different resistance genes were found in bacteria carried by the Yanomami, an indigenous group in the Amazon thought to have been isolated until researchers contacted them in 2009. Resistance has also been identified in mummified human remains from Peru dating to the 11th century.
These genes are not just pervasive in nature – they are also being passed around in unexpected ways. An abundance of resistance genes has been found in bacteria floating in Beijing’s smog. A survey of developing countries identified chicken coops and urban wastewater treatment facilities as potential “hot spots” for the swapping of resistance genes.
The ocean, home to an incredible diversity of dissolved chemistry, also acts as a reservoir for these genes, and researchers are trying to figure out if they move from the seas into the human population. So who better to study than surfers?
“A lot of the research of the transmission of resistant bacteria has focused on the role of the health care environment,” said Anne Leonard, an environmental epidemiologist at the University of Exeter who is investigating whether surfers have higher rates of bacterial colonization. “What’s less well studied is the role that natural environments play.”
By some estimates, surfers can swallow about 170 milliliters (5 3/4 ounces) of seawater per session. Leonard and William Gaze, of the European Center for Environment and Human Health, and his colleagues have estimated that recreational swimmers and surfers in England and Wales may be exposed to resistant strains of E. coli in the ocean on more than 6 million occasions each year.
Because bacteria readily pick up and pass on genetic information across species, researchers suspect the risks of acquiring resistant genes are higher in places that facilitate direct transfer with microbes inhabiting the body. Coastal waters polluted with sewage, in this view, are probably more worrisome than smog or deep caves.
At the moment, no one is sure whether it is actually possible for people to pick up these microbial genes from a long day at the beach. In the lab, however, Kapono has found evidence for the transfer of resistance genes from bacteria in the ocean into strains associated with the human gut when they are placed in proximity.
Evolutionary pressures favored the emergence of resistant genes. Microbes are drawing upon this natural bank of resistance today to fend off the best drugs devised by humans.
“These antibiotic resistance genes did not arise in order to make our lives awkward,” Hanage said. “They have completely different functions that only have recently been repurposed.”
“These things are everywhere,” he added. “If we want to stop them from moving into pathogens that are killing us, we need to understand where they are.”
Back in California, Kapono has begun analyzing the data from his globe-trotting quest. So far, neither he nor his collaborators have found evidence that swimmers or surfers are picking up antibiotic-resistant infections from the ocean.
But Kapono noticed in his preliminary data that certain metabolites from his body came to resemble those of other local surfers as he moved from region to region. That could be a result of commonalities in diet or lifestyle – or it could be evidence that immersing our bodies in saline, microbe-rich environments has a detectable biochemical impact.
Kapono has taken samples from surfers in California and Hawaii; surfers in the South Pacific are next. He is mulling a trip to Chile to conduct field work at Punta de Lobos. The rural location may yield some unique microbes.