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Today, heart transplant patients must wait months or longer for a donor organ to become available.

Custom Organs, Printed to Order

Eight years ago, Stephen and Amelie Trice learned that their three-year-old son Troupe needed a new heart. After many months of perplexing symptoms—small size, low energy, enlarged liver—Troupe was diagnosed with restrictive cardiomyopathy, an extremely rare and deadly condition in which the heart is unable to relax between heartbeats. There is no cure and very few treatments. Despite his doctors’ attempts to manage his condition with medicine, Troupe’s health deteriorated. Afraid of losing their son, the Trices sought the expertise of a cardiologist at Children’s Hospital in Atlanta. The doctor sat the worried parents down and over two hours explained that Troupe needed a heart transplant. Amelie recalls, “With a diagnosis of certain death, our only option was to cross our fingers that we were going to get more time with a new heart.” The Trices went back home to Alabama, explained what they had learned as best they could to Troupe, and waited. Two months later, the couple were out with friends when they got the call. “Across the table [Stephen] yelled to me, ‘Amelie, they got a heart for Troupe!’ I didn’t say goodbye or pay a tab. I literally picked up my purse, walked out of the restaurant, and got into the car.” The next morning, Troupe was in surgery. Amelie, a registered nurse, knew that soon the surgeons would be cracking open their toddler’s chest. Another thought weighed on her mind, too. “As I walked to the waiting room unable to stop the tears and the feeling of my knees buckling, I knew that somewhere a mother and a family was grieving for their baby.” Four weeks later, Troupe’s heart was still not working as it should. Again, he was dying. Quickly, doctors found a second organ and performed an emergency surgery. This time the transplant took. Still, Amelie remains haunted. “I live with a complex ball of guilt and grief,” Amelie says. “I benefited from someone else’s pain.” At Troupe’s tenth birthday celebration, while he skated with his friends, chatted up his family, and scarfed pizza, the heart of another child pumped blood into his lungs, through his body, and back again. But the Trices’ could not relax. The family had learned that again they would need the generosity of another despairing family—their youngest son Henry would also need a new heart. Thankfully, last year, Henry received his match. According to Stephen, when the Trice family began their relationship with the United Network for Organ Sharing, “the average wait for a child’s heart was six months. The current average wait for a child of Henry’s size is one year.” In the United States, and worldwide, we face an organ shortage. Today, over 123,000 people in the U.S. are waiting for lifesaving organs, according to the network. Many patients will never receive a match. “Only about 14,000 people in the entire United States are suitable for organ donation.” Right now, only a human body can grow a complex human organ. Unlike relatively simple tissues such as bones and skin, to give a heart, the donor must be declared brain dead and the family must consent. According to Howard Nathan, the president and CEO of Gift of Life, the nonprofit group appointed by the U.S. government to match transplant donors with those in need, 2.4 million people die in the United States every year. About half die in acute care hospitals where organs can be obtained. Of that roughly 1.2 million people, only 1% are suitable for organ donation. “That’s it,” he says. “Only about 14,000 people in the entire United States are suitable for organ donation. 8,200 people last year were donors.” Faced with those numbers, scientists and doctors have begun to ask, what would it take to give a family like the Trices a pair of new hearts without guilt or delay? Currently, tissue engineering can provide simple, thin tissues including cartilage, skin, and bone. Larger, more complex organs like the liver and heart present much more formidable challenges. They are structurally intricate, contain many different cell types, and require an extensive network of blood vessels. Some researchers are working to create useable organs within animals. Much of this work has focused on genetically engineering animals such as pigs to grow human-compatible organs. But while researchers have succeeded in engineering pig organs to express human cell-membrane proteins, over time, additional incompatibilities have emerged. Some which were implanted in non-human primates suffered from immune attacks. Others failed due to incompatibilities with blood clotting proteins, which can cause blockages in some places and uncontrolled bleeding in others. The fact remains that today, if someone needs a complex organ, a human is required to provide it. But in the near future, perhaps, families may not have to live with conflicting emotions of guilt, grief, and joy. Maybe all that will be required are a knowledgeable team of dedicated people, a slurry of cells, and a printer. <h2> Bioprinting in 3D </h2> Around the time that Troupe Trice was undergoing surgery to receive his new heart, Dr. Thomas Boland at Clemson University secured a promising sounding patent: “Ink-jet Printing of Viable Cells.” Boland’s patent relies on 3D printers, which can build complex shapes from little more than blueprints and the right type of material, including cells. An ink-jet printer that spits out three-dimensional objects works much like the familiar two-dimensional versions that sit on our desks—in fact, many started their “lives” printing paper. Like the 2D version, a 3D printer precisely deposits material drop by drop. But instead of feeding a sheet of paper past the print heads, a 3D ink-jet printer ratchets its platform down a notch and then deposits another layer atop the last. The “ink” can be virtually anything that can flow through a print-head and later harden—plastic, wood pulp, proteins, human cells. For 3D bioprinting, scientists fill the ink cartridges with cells and proteins instead of plastic. There’s also another promising 3D bioprinting technology, called stereolithography, which uses laser light to harden portions of a soup of polymers into a solid frame or “scaffold.” When the machine is done, the excess liquid drains away to expose detailed supports. Researchers then bathe these scaffolds in cells and nutrients and wait for the cells to grow and remodel the scaffold to their liking. Organovo's bioprinter creates tissue that mimics the structure and composition of various human organs. Like many 3D printing techniques, 3D stereolithography was originally designed for more traditional manufacturing. There, the usual polymer materials are efficient, but unsuited to printing organs. “No matter how convenient the 3D printing technology may be, if there are toxicity aspects remaining, it is essentially useless for real life applications,” says Sungho Jin, a professor of materials science at the University of California, San Diego. Roger Narayan, a biomedical researcher at North Carolina State University, set out to make them biocompatible, so he substituted riboflavin—or vitamin B12—for the toxic polymer hardening substances. In one set of experiments, he found that the structures were less toxic than glass, meaning the mixture would be suitable for implantable medical devices or possibly as scaffold for fine-featured organs. “What is unique about this technique,” Narayan says, “is that it allows you to do 3D printing at submicron dimensions. You begin to be able to make structures that can interact with cellular or sub-cellular components.” That high resolution allows researchers to consider 3D printing tissue types that were too detailed for earlier methods. “Many tissues exhibit complex small-scale geometries that are difficult for engineering to mimic using conventional scaffold techniques,” says Mohan Edirisinghe, a biomechanical engineer at University College London. “Complex scaffolds for many types of artificial tissues, including the kidney, the liver, and blood vessels, can be created using this approach.” Narayan’s technique and its kin are still early in their development, but there is one company that’s 3D printing tissues today. San Diego-based Organovo is using 3D tissue printing to create 3D printed “organs on a chip.” Rather than spending time and money testing drugs on animals, organs on a chip will allow researchers to test immediately on human cells. Cells can come from a research cell line, a patient, or other sources such as stem cells. “These tissues will take the form of both normal health or diseased by design,” says Michael Renard, executive vice president of commercial operations. Organovo’s has released a 3D-printed liver tissue, and the company has partnered with the NIH to create tests for human eye tissue as well. <h2> State-of-the-Art </h2> Organovo liver tissues, while an impressive 20–30 cell layers thick, are not fully-functional organs, but they are a step toward that goal. Several challenges remain, Renard says, including “securing the proper cell types in the quantities needed to achieve the desired level of function and the integration of a vascular network necessary to maintain a healthy condition.” These hurdles are shared by virtually anyone hoping to create complex human organs. Robert Langer, a professor of chemical engineering at MIT, points out several other oft-forgotten limitations of 3D bioprinting. “Right now, we can’t make any organ or tissue to function properly in humans other than skin. 3D printing hasn’t even been used successfully for that. Making an organ also requires blood vessels, nerves, and cells to behave properly. 3D printing can’t do that.” Recreating human vasculature, seen here in a 3D CT scan of a human heart, is difficult using current 3D printing techniques. Still, the desire to print these organs drives much of today’s 3D bioprinting research. Laboratories have successfully recreated human ears, noses, skull bones, jaw bones, tracheas, ears, noses, skin sections, bladders, arteries, and fat. Rather than cutting squares of healthy skin from a patient to help cover an injury, a 3D printer could print skin perfectly shaped to fit. Patients marred by disfigurement may soon be able to customize a nose on a computer. While some 3D printed body parts, such as skull and facial implants, have shown success in human patients and have received FDA approval, others are still working their way from the laboratory into animal testing. Few tissues are ready for implantation. Size remains a problem, Renard says. Current technologies struggle to build tiny structures such as human retinas, capillaries, and ear cochlea, as well as large, complex organs like livers and lungs. If you need fine detail, it takes so long to build an organ that the cells die. If a researcher quickly prints a large organ from huge blobs of cells, she cannot engineer enough detail to provide blood vessels for the cells to survive, for example. In many ways, the challenges of 3D organ printing mirror those of organ transplantation. As Nathan from Gift of Life points out, “When taken from a deceased person, tissues can be collected 24 hours after the heart stops, but organs need a blood supply.” Without vasculature, cells do not receive nutrients and oxygen or excrete wastes beyond a thickness of a few layers. “One of the greatest challenges is ensuring that printed structures have an adequate supply of nutrients and oxygen until they can integrate with the body,” says Dr. Anthony Atala, the director of the Wake Forest Institute for Regenerative Medicine. Researchers have been scrambling to find ways to fix this plumbing problem. Strategies include layering cells on pre-made channels, leaving holes in tissues for blood vessels to grow, and adding chemicals that encourage blood vessel formation. A stained sample of Organovo's 3D printed human liver tissue Tissues are somewhat easier than organs. Cartilage, for example, does not need as much blood as other tissues, which is partly why Faiz Bhora, chief of thoracic surgery at Mount Sinai Roosevelt and Mount Sinai St. Luke’s Hospitals in New York City, is working to 3D print a working trachea from stem cells. Bhora begins by using a gel that is hardened with UV light to create the scaffold. He then seeds the scaffold with stem cells and adds signaling compounds which instruct the cells to turn into cartilage. As a test, the team implanted a printed trachea into a baby pig. It is now a healthy adult. Bhora hopes to gain FDA approval of the first 3D bioprinted artificial trachea within three years. At Cornell University, biomedical engineering professor Jonathan Butcher is working to build a functional human heart valve. His team starts with a goopy liquid the consistency of toothpaste that contains stem cells, hydrogels, and nutrients, and then they harden the liquid to the perfect stiffness using light. As he’s perfected the system, Butcher has reduced the time required to build a heart valve from 14 hours—long enough for all the cells to expire—to under an hour. “One hour is more than enough. The cells don’t really care about that,” he says. Rather than placing each cell in the valve exactly where it needs to go and telling each cell what it needs to do, Butcher is betting that if he puts the stem cells in the right environment, they will figure it out. As a part of the process, the cells are trained and tested in a machine that simulates human blood flow before they are implanted in an animal or human. “You have to figure out how to make this thing so that right when you implant it, it is working,” he says. “We are pirating the natural engineering.” <h2> An Agonizing Wait </h2> Thirty years ago, 3D printing was just an experimental technology capable of producing rudimentary objects. Today, researchers are cranking out organ scaffolds that are orders of magnitude more complex. While that progress has been remarkable, we still have a long way to go. We’re nowhere near growing a little heart for a child like Trice or Henry, a liver for a beloved parent, or a kidney for a tiny infant, Atala says. “Based on our current work, we expect segments of bone, muscle and cartilage to be available within five to ten years. More complex structures, such as kidneys and livers, will obviously take much longer.” That day cannot come soon enough for those who are waiting for organs, but for now they must hope for a human match. “I try not to worry about whether we will get one in time, and just continue on day to day,” says Amelie Trice. Still, the promise of the technology makes her hopeful. “My greatest wish is someone will grow a new healthy heart, customized to my children’s immune systems and bodies, so we would never need a donor or medications that have so many side effects, and they could live long and happy lives naturally.” Image credits: Gordon Museum/Wellcome Images (CC BY-NC-ND), Courtesy Oganovo, Mark Riccio

Replacing a failing kidney or scarred heart may soon require little more than a slurry of cells and a 3D printer.

Should We Study Human Embryos Beyond 14 Days?

To talk about pregnancy, we should first talk about frogs. Frogs spawn hundreds of eggs in water that is teeming with parasites and predators. In some species these eggs grow at breakneck speed, transforming from one fertilized cell to the 40 million that make up an independently swimming tadpole in about two days. Errors are common. Most do not survive. We have evolved a different strategy. We devote all of our reproductive energies to one embryo (usually). But we lose them all the same. Despite years of study, we don’t fully understand why as many as 30% of pregnancies fail or why some women suffer more misfortune than others. A nine to ten week-old human embryo Thanks to IVF, the days leading up to implantation are well-studied. With IVF, at around seven days post fertilization, healthy embryos are squirted into the potential mother’s uterus in the hopes that they will burrow into the lining and grow. If successful, the embryo dives in and disappears. Scientists describe the period that immediately follows as a black box. What little we do know is based on donated and preserved human embryos made available through institutions like the Carnegie Collection, started in the early 1900s, and the cultured embryos of animals–mice, chicks, the rare large mammal, and a few non-human primates. But humans are not frogs or mice or monkeys, and so to understand human development, we have to study humans. It’s no easy task. The newly implanted embryo is like a grain of sand embedded in a pillow locked in a box—impossible to observe. Unless that is, you can get an embryo to develop not in a uterus, but in a dish. <h2> Limits </h2> This summer two collaborating laboratories did just that. Headed by Ali Brivanlou, a professor at Rockefeller University, and Magdalena Zernicka-Goetz, a professor at the University of Cambridge, they published in Nature and Nature Cell Biology the first ever images of live human embryos cultured to days ten, 11, 12, and 13. Embryos at this stage usually die if not nestled in the uterine wall. “This is a stage that is difficult to study in mice,” Zernicka-Goetz says. “It is next to impossible to study in humans.” But this time, the researchers had created a sufficient surrogate—a little shelter that allowed the human embryos to be bathed in just the right solution. They watched them grow. The previous record had been nine days. Most groups could not get past seven. “We discovered, in the human embryo, a population of cells that nobody else has ever seen in any other animal. Not knowing that this is part of our anatomy—at the beginning of the 21 st century—is a little bit, how shall I say, embarrassing,” Brivanlou says. Mouse studies had left them so ill-prepared that according to Brivanlou, “it should no longer be qualified as the closest model to humans.” Brivanlou thinks that embryonic self-organization may continue well past 13–14 days post-fertilization, though he cannot be sure. When the embryo reached 13 days, his lab stopped the experiment. The embryos were frozen for reasons of research ethics. They had bumped up against the 14-day rule. <h2> Origins </h2> The 14-day rule is an ethical line past which cultured human embryos are not to continue developing outside the body. It is protected by law in 12 countries, including the United Kingdom, and acts as a guideline in five, including the United States. The rule was created shortly after the birth of Louise Brown, the first IVF baby, in 1978. An ethics advisory board was called to make broader recommendations for the treatment of human embryos in research and in IVF clinics. Leroy Walters, then the director of the Center for Bioethics at Georgetown University’s Kennedy Institute, was on the advisory board at the time. “We were all pondering, well, what would be a good upper limit? For a variety of reasons we came to a consensus that 14 days was a reasonable limit, even though that was way beyond what anyone had been able to achieve.” One of those reasons was that pre-implantation embryos are regularly discarded by the human body. In the language of the report, “not every meeting of sperm and ovum results in the production of a viable embryo. One study estimates that...only 37% of fertilized human eggs survive to be delivered as live infants.” Another consideration, Walters says, was that “embryos before the completion of implantation can split into two and give rise to twins, or more rarely, two embryos with different genomes can combine into a single hybrid embryo.” Some argued, how could an embryo at this stage represent a person if it could become two people or two could become one? “We were all pondering, well, what would be a good upper limit?” Fourteen days is also about the time when a human embryo elongates and develops a line called the primitive streak, which marks a channel where the spinal cord will eventually grow, Brivanlou says. “In other words, it’s that moment in your life—actually the most important moment in your life, not divorce, or marriage or kids—it’s that moment where you separate your head away from your butt.” This development of individuality, of head and butt separation, is a key rationale behind the rule. But is it the correct goalpost? In the same issue as the report documenting the first 13-day human embryo culture, Nature published a commentary calling on scientists and ethicists to reconsider the 14-day rule: “In light of the evolving science and its potential benefits, it is important that regulators and concerned citizens reflect on the nature of the restriction and re-evaluate its pros and cons.” Pushing past 14 days to, say, 21 or 28 days could help doctors understand and possibly prevent and treat a vast swath of medical problems, including infertility, pregnancy loss, spina bifida, cancer, and various diseases of aging. It would likely lead to improved stem cell therapies for today’s intractable diseases, such as diabetes, Parkinson’s, and multiple sclerosis. Other tantalizing possibilities include better understanding of fetal alcohol syndrome, potential causes of autism, how and why some chemicals affect development, and the strange and heartbreaking birth defects caused by the Zika virus. The researchers have already learned a great deal by watching embryos develop up to 13 days. “I almost fell off my chair,” Brivanlou recalls—not just because he was witnessing something so few had ever seen, but because what he saw was so surprising. “I always believed that the minute the embryo attaches to the uterine wall, the interactions between the embryonic tissue and the maternal tissue will have to coordinate so that everything happens within the correct timing. What we saw here was that at least for the first 13 days or so, all the information that is necessary and sufficient to generate all the cell types is actually within the embryo, not from outside.” It was like the human embryo was a snowflake, creating a mesmerizingly complex structure from itself alone. “That to me was one of those amazing moments in my scientific career,” Brivanlou says. <h2> Loss </h2> Perhaps the most immediately apparent benefit of pushing past the 14-day limit is in better understanding and preventing early pregnancy loss. Early pregnancy loss, commonly called miscarriage, is when a pregnancy spontaneously terminates during the first 13 weeks. While most pregnancies that fail that early are never known, about 10% of known pregnancies result in early pregnancy loss and one-third of pregnancies result in miscarriage for women over 40, according to the American College of Obstetricians and Gynecologists. For those trying to get pregnant through IVF, 70% of conceptions fail. Because of the risk of miscarriage, women are often counseled by friends and the internet not to announce a new pregnancy until around the third month. But not talking about it doesn’t make less common, nor does it erase the experience. Miscarriage can cause enormous emotional stress to women and their families. Maria Dunlap lives in the western U.S. with her husband and two naturally conceived, biological children. Her first pregnancy, though, didn’t go as hoped. She and her husband had quickly become pregnant, but at about seven weeks, she began to bleed and realized that she was suffering a miscarriage. Ten (left) and 11 (right) day-old human embryos “The emotional toll was extremely heavy and way crazier than I thought it would be. When I was going to the grocery store I couldn’t even walk down the aisles that had baby supplies because I would just cry.” Charlotte Emery lives in South Carolina with her husband and three biological children—a daughter and twin boys. She had several miscarriages before she was diagnosed with a genetic blood clotting disorder. She talks about the toll of miscarriage on her previous relationship. “We went into opposite corners of life...There becomes this whole emotional roller coaster where you are looking at your partner, and you are saying oh, well, it’s us, it’s you, it’s everything. We just grew apart in a big bad way.” Just up the coast, Erica Kim lives in suburban Virginia with her husband and two adopted children. She has suffered four pregnancy losses, spent an estimated $75,000 of personal money trying to conceive through scientific means, and had zero live births. Erica says she can talk openly about her experiences only because of support from family and professional therapy. “When you are unable to do something that is so fundamental to the human body and mammals, all mammals, to procreate, to have your own offspring...Unless you are superhuman and don’t have emotions, anyone who goes through that suffers keenly. I think I developed PTSD from pregnancy loss.” <h2> Limbo </h2> Of course Dunlap, Kim, and Emery’s pregnancies had progressed beyond 14 days, long enough that the women were aware they were pregnant. Many women share the same experience, nurturing embryos that will never progress to a live birth. In cases of natural conception, nonviable embryos are flushed away in monthly menses; with IVF, unused embryos may be frozen or destroyed. It’s important to remember how many fertilized eggs are discarded by human bodies, even before a woman knows she is pregnant—and well past 14 days, says University of Manchester bioethicist John Harris. “If God or nature regards embryos essentially as expendable in order for healthy human adults first to come to term as embryos and then to grow up, it is unclear to me why we should have a rule as restrictive as the 14-day rule,” he says. “What I think we need is a much clearer discussion about when and why the emerging human individual becomes morally significant—becomes the sort of thing that could have rights or interests.” “If God or nature regards embryos essentially as expendable, it is unclear to me why we should have a rule as restrictive as the 14-day rule.” Many researchers point out that, for the embryos they work with, the alternative to allowing them to develop further is usually destruction. “The only human embryos we study are ones discarded from the IVF clinic that would never be allowed to develop into babies,” Zernicka-Goetz says. “It is believed that 70% of these would fail in their development. To work on these embryos, we have full agreement of the donor couples.” Today, over five million babies owe their existence to IVF, and one of the results of those successes are the embryos that remain frozen, hundreds of thousands of which are in the U.S. alone. Many patients will ultimately choose to donate their unused embryos for scientific research. In other cases, healthy IVF embryos are given to infertile couples for the creation of children. Maria Dunlap knows one of these babies. “I actually have a girlfriend here who adopted IVF embryos from somebody else who was done having their kids and had a bunch of extra embryos. And now she has a two-year-old daughter who plays with my son.” But this alternative is rare, and some U.S. studies show that women and couples hesitate to hand over their embryos to strangers for the purpose of creating a child. Erica Kim’s experience affirms the sentiment. “We felt uneasy donating them to another couple that would potentially raise our biological child.” For Dunlap, the challenge is reconciling her faith with the advances that research could provide. “If a person believes that even an embryo at day one is already a human being—even if it is just presenting as a cluster of cells—then you have to follow the logic through and say, well now it’s not OK to destroy that, day one, day nine, day 14. From a science perspective, I love the idea of learning more about what you could do to prevent people from losing pregnancies at any stage. I am very pro-science. But then I’m super, super pro-baby.” <h2> Debate </h2> Some critics view calls to re-evaluate the 14-day rule as a pernicious moving of the goalposts. How meaningful can they be, the line of reasoning goes, if scientists want to change rules as soon as they bump up against them? “There were disagreements about the rationale and validity of the 14-day rule before this point, but no one in the research community really pushed the issue because it was not particularly important,” says Glenn Cohen, a Harvard bioethicist. “There is nothing wrong with pragmatic necessity driving us to start a re-examination process.” Revision is not necessarily a bad thing, says Debra Mathews of the Johns Hopkins Berman Institute of Bioethics. Plus, scientists are not the only ones whose views may change. “There are many processes wherein we make a decision, we collect information, and we revise our decision. I don’t think that’s actually a problem. When Louise Brown, the first IVF baby, was born—the uproar! And now 2% of babies born in the US are born by IVF.” The potential for scientific advancements should be considered when determining the ethics of human embryo research, Mathews says. “It’s weighing social, moral, ethical concerns against the value of the science.” For those who oppose human embryo research at any stage, such arguments may seem irrelevant. “Young human beings, especially in their unique vulnerability during early stages of development, are ‘ends’ in themselves, entitled to unconditional respect and protection, not ‘means’ to be utilized to achieve other goals, even when those goals may be lofty and high-minded,” says Father Tad Pacholczyk, director of education at the National Catholic Bioethics Center. Stacy Trasancos, an author and mother with advanced degrees in chemistry and theology, says that, as a Catholic, she believes an embryo at any stage is deserving of full human rights. “We oppose any kind of research that uses human lives as research products or commodities,” Trasancos says. “We come back to the extreme case—would you do it with two-year-olds?” Regarding the argument that embryos are naturally discarded from the body, and miscarriage is common, “there’s a difference in a natural death and intentional killing,” she says. Researchers know that any change could be contentious, and they are clear that they do not want any change without a transparent public conversation. “My job right now is to make sure that the debate is initiated,” Brivanlou says. “This is too important of a topic to leave it in the hands of scientists alone. In fact, scientists should be ex officio sitting on the sidelines, ready to answer questions required to make a decision but not necessarily be part of the decision itself.” Trasancos agrees that the conversation is important. “I do think there needs to be an all-encompassing conversation,” she says. “It’s about the dignity of human life.” Brivanlou is similarly reverent, using words like “beautiful” and “mesmerizing” to describe what he sees in his research. “I have you tell you one of the toughest decisions in my life was when I had to pull the plug after this whole thing, because I realized that this Pandora’s box has not even been explored—not even a piece of dust of it has been explored yet.” Image credits: <a href="https://www.flickr.com/photos/lunarcaustic/2433149102/"> lunar caustic/Flickr (CC BY-SA) </a> , Gist Croft, Alessia Deglincerti, and Ali H. Brivanlou/The Rockefeller University, Zernick-Goetz/University of Cambridge

Studying human embryos after 14 days of development could be illuminating, but ethical questions abound.

Beyond Antibiotics

Late on the night of December 26, just three days after I had given birth to my son and two days after receiving two blood transfusions for complications, I was back in the hospital. This time, I had gone straight to the emergency room. There we were: me, my days-old baby, and my husband. The ER doctors put us in a separate room to try to isolate us from the contagion filling the hospital floor. But a few hours in, my husband started vomiting. He was asked to leave if he did not wish to become a patient. My baby could not stay with me. It was dangerous just having him there. I was alone. I had left the hospital with my baby on Christmas Day. As best I can recall, the discharge nurses had instructed me to call back if I developed a fever over 101 ̊ F. The day I checked into the ER, our thermometer had read just a few tenths of a degree over. In many ways, a hospital acquired infection has become more serious than an uncontrolled bleed. The doctors knew I had recently been in the hospital, and they knew that I had lost a lot of blood. But they had no idea which bacterial strain was causing the fever, so they hedged their bets, giving me two different antibiotics—one for MRSA (methicillin-resistant Staphylococcus aureus ), a common antibiotic-resistant strain of staph bacteria, and another antibiotic for the common infection culprit E. coli . When my hospital roommate heard I was on a drug for MRSA, she requested to be moved. I lay in bed alone, ordered hospital food, and pumped tainted breast milk. In the days that followed, I started eating ice in the hopes that it would trick the nurses’ thermometer and they would let me go home. I fooled no one. This low-grade fever would keep me in the hospital for twice as long as my massive blood loss did following birth. My two hospital stays illustrate how the script for medical care has flipped over the last several decades. In many ways, a hospital acquired infection has become more serious than an uncontrolled bleed. Bacteria and other pathogens are developing multi-drug resistance, and our last, best strategies are failing. You may have heard the rumblings. Doctors have been warned not to over-prescribe antibiotics. Consumers have been admonished against the antibacterial soaps and creams. We can now buy meat and dairy marked “animals not treated with antibiotics or hormones” in the supermarket. But those measures are only stop-gaps. They will only, perhaps, slow the pace of resistance. For years, researchers and doctors have known this. Responsible antibiotic use isn’t enough to win the pathogen war—it “reflects an alarming lack of respect for the incredible power of microbes,” wrote a group of infectious disease experts from across the U.S. in a 2008 “ <a href="http://cid.oxfordjournals.org/content/46/2/155.long"> Call to Action </a> ” paper. After all, they write, microbes have been evolving and adapting for 3.5 billion years. Thanks to their combination of genetic plasticity and rapid generation time—they can undergo as many as 500,000 generations during one of ours—they are especially good at overcoming evolutionary obstacles. “We don’t have really a plan B.” Antibiotic resistance is just another byproduct of those abilities. It has evolved because patients don’t complete a full course of drugs or because animals receive drugs they don’t really need or because a college kid slathers his apartment in antibacterial spray. Antibiotics kill most but not all of the bacteria they encounter. The strongest ones live. These reproduce and pass on their advantages, and sometimes they get together and swap genes. Eventually, the resistant types grow very, very resistant. It wouldn’t be a problem if bacteria weren’t evolving resistance faster than we have been able to respond. New antibiotics are difficult to produce, and they don’t make as much profit as drugs for chronic disease, so there has been a dearth of investment. “Why it feels like it’s happening right now is that there aren’t really new antibiotics coming down the pipeline,” says Dr. Carmen Cordova, a microbiologist who works for the nonprofit National Resources Defense Council. “We don’t have really a plan B.” Three years ago, science journalist Maryn McKenna published <a href="https://medium.com/@fernnews/imagining-the-post-antibiotics-future-892b57499e77"> an award-winning article </a> in which she imagines a modern environment devoid of antibiotics. It’s a return to the medical dark ages in which illnesses like tuberculosis, pneumonia, and meningitis are death sentences. It would mean that burn victims, surgery patients, laboring mothers, and those undergoing chemotherapy would have to worry constantly about succumbing to infection. President Barack Obama has called antibiotic resistance “one of the most pressing public health issues facing the world today.” A conservative estimate from a British project called the <a href="http://amr-review.org/sites/default/files/AMR%20Review%20Paper%20-%20Tackling%20a%20crisis%20for%20the%20health%20and%20wealth%20of%20nations_1.pdf"> Review on Antimicrobial Resistance </a> states that, if left unchecked, antibiotic resistance will cause 10 million human deaths per year—more than the number of people who currently die from cancer and diabetes combined. The threat is looming. Late last year researchers identified bacteria resistant to a last-resort antibiotic in Chinese raw chicken and pork meat, slaughterhouse pigs, and hospital patients. The resistant gene has since been identified in bacteria across Asia and Europe. But we are fighting back. President Obama has asked Congress for $1.2 billion over five years for developing new diagnostic tools, creating a database of antibiotic resistant diseases, and funding research to better understand drug resistance. It joins other, ongoing efforts to identify promising new candidates. In labs and universities around the world, researchers are hard at work identifying, testing, and perfecting strategies that go well beyond what, today, we call antibiotics. <h2> Knocking Out Communications </h2> We used to think that bacteria were dumb. We thought they ate, pooped, divided, and not much else. We now know that this story is much too simple. Bacteria communicate, keep tabs on their environment, and respond and react. They ask how many others are around and how they are doing, and only when a certain number have congregated do most pathogenic bacteria turn virulent. The danger is in numbers. Of course, sometimes they gain the upper hand despite our best efforts. But what if there was a way to hide them from one another? What if we could shut down their party before it starts? That’s the idea behind quorum sensing inhibitors. Quorum sensing inhibitors (QSIs) are molecules designed to interfere with pathogen communication. When bacteria go looking for friends, they put out small molecules like little flags, saying, “I am here!” For the past two decades, researchers have been working to develop strategies that interfere with every step of the process, by halting production of these flags, obscuring them so that other bacteria cannot recognize them, or blocking responses when they are recognized. The results, so far, have been promising. According to Vipin Kalia, a researcher at the Institute of Genomics and Integrative Biology in Delhi India, such quorum sensing inhibitors are less likely to lead to bacterial resistance because, “Antibiotics create a pressure on bacteria because their survival is under threat. QSIs are not threatening their existence and survival.” Several of these inhibitors have been shown to reduce virulence in animals, Kalia says, and two have made it to clinical trials. Still, none are currently used to treat human diseases, and while it may be more difficult for bacteria to develop resistance to these inhibitors, it is not impossible. In fact, it may already be happening. In a 2014 paper in the journal Microbial Ecology , Kalia and his colleagues write that “evidence is accumulating that bacteria may develop resistance to QSIs.” It appears that communication is important enough to bacteria that they have several different channels. If one path is blocked, they try to use another. “Apparently” the researchers write, “bacteria do not even need to undergo any genetic change to withstand quorum sensing inhibitors.” QSIs may buy us some time, but will it be enough? Fortunately, there are other options. <h2> Creating an Inhospitable Environment </h2> The development of new antibiotics has often relied on tweaking existing drugs. It’s a simpler approach than developing an entirely new class of antibiotics, but the modifications are often small enough that bacteria can adapt relatively easily. Fortunately, plants, animals, fungi, and other microbes have been battling it out long before we arrived, and they have evolved a few good tricks. One, antimicrobial peptides (AMPs), were first identified in silk moths and are now known to be an innate immune response in almost all organisms from algae and plants to the entire animal kingdom. AMPs use differences between the membranes of a host cell and a bacteria to selectively target only the harmful microbe invader. Bacteria tend to be negatively charged, while mammalian cells tend to be neutral. The positively charged peptides glom onto the bacteria’s membrane and punch holes in it. Rather than having to recognize specific targets on the cell membrane, as traditional antibiotics do, AMPs grab any bacterial membrane that doesn’t belong and shoot it full of holes. AMPs happen to be much more resistant to bacterial adaptations. Despite their ancient origins, AMPs remain effective weapons today. “Bacteria can become resistant to antibiotics by simple modifications of the receptor where the drug attacks. To become resistant to AMPs...they need to change their entire membrane chemistry,” says Karen Lienkamp, a junior research group leader working on AMPs at the University of Freiburg in Germany. Right now, researchers are working on making materials that have synthetic versions of AMPs, or SAMPs, on the surface. These specially engineered surfaces help reduce microbe contamination on hospital equipment, in the air, and on clothing. Specifically, they prevent biofilms—clumps of bacteria that form protective nets around themselves. “Biofilms are the ‘root of all evil,’ ” Lienkamp says. “Studies with regular antibiotics have shown that you need up to 1,000 times the concentration to kill bacteria that are encapsulated in a biofilm.” Other strategies to prevent bacteria from taking up residence on hospital surfaces include extra-slippery materials and materials that shed layers to prevent buildup. Yet as promising as they are, anti-fouling surfaces are only useful for prevention. They won’t help someone who already has rampant infection. What we really need are ways to identify what ails us, and quickly, with customizable drugs to treat them. <h2> Faster Identification </h2> Justin O’Grady is a lecturer in medical microbiology at the University of East Anglia in the United Kingdom. Last year, he and others published a paper in the journal Nature Biotechnology about a technology that can take a sample of blood and, in six to eight hours, identify the bacteria that is causing an infection. In hospitals and labs today, it typically takes two to five days. The device is a gene sequencer called the MinION, which reads the bacteria’s genetic signature within minutes. It’s small enough to plug into a computer’s USB drive, and at around $1,000 for the necessary equipment, it doesn’t cost nearly as much as traditional laboratory-grade gene sequencers. Moreover, the device, when given another day or so to process the sample, can also identify which genes in an invading bacteria are responsible for the antibiotic resistance. “This would be a personalized medicine approach to antibiotic treatment,” O’Grady says. While other molecular identification technologies exist, sequencing technologies like the MinION are broad-spectrum microbe detectors. “The advantage of sequencing for this approach is that you get an unbiased diagnosis,” O’Grady says. “You don’t need to know anything about what pathogen might be in there.” If something like MinION had been available when I was in the hospital, my experience would probably have been quite different. It wouldn’t have taken doctors five days to determine the root cause, getting me home sooner and saving both the hospital and the insurance company a significant amount of money. I also would not have been administered ineffective antibiotics, preventing a small amount of evolved resistance. Instead of doctors treating their patients with best-guess antibiotics while they wait days for culture results to come back, sequencing technologies like these will tell them what is going on by the time the nurse comes around with the second dose. “If we can change the way that we prescribe antibiotics, we can improve antibiotic stewardship and we can improve patient management at the same time.” O’Grady says. “The patient receives better treatment quicker, and society benefits because we keep our potent antibiotics for those who need them most.” <h2> Building a Library </h2> The most promising new antibiotics may, counterintuitively, come from the bacterial domain itself. Though nature’s bacterial library could hold a multitude of undiscovered antibiotic recipes, sifting through its diversity is a daunting task: Most bacteria found in the environment—99%—will not grow on a petri dish in traditional cell culture. We may soon be able to unlock that library, though, thanks to the work of Kim Lewis, director of the Antimicrobial Discovery Center at Northeastern University in Boston. Lewis reported last year in the journal Nature that he and his colleagues found a way to culture bacteria from the soil, which have been notoriously difficult to grow in the lab because they rely on signals and molecules from neighboring bacteria to grow. Lewis and his colleagues decided that rather than try to painstakingly recreate those conditions, they would just bring a little soil back to the lab. They started by collecting a small scoop of soil, rinsing it in water, mixing the water into culture medium, and then squirting the mixture into a device they developed called the iChip. They then placed the iChip into a bucket of the same soil kept in the lab. After a month they pulled the iChip out, cultured the bacteria, and observed what was growing. The bacteria were still growing in agar—not their ideal environment—but they were happier after the month spent back in the soil. “Ten percent of uncultured bacteria from the natural environment require growth factors from neighboring bacteria,” Lewis says. Their soil vacation seems to make the bacteria stronger, more adaptable, and more likely to grow on the iChip. Eager to build their library, Lewis and his colleagues began collecting from their back yards. If someone went on vacation, they were given a kit to bring back a sample. One collaborator took a serendipitous trip to Maine and returned with a completely new genus of bacteria, one that produced an incredibly effective antibiotic that kills other types of bacteria, which they named teixobactin. In experiments with human cells and in mice, teixobactin proved exceptionally effective at killing Clostridium difficile (a resistant bacteria that causes ulcers and is most effectively treated with fecal transplants) and Staphylococcus aureus , the bacteria whose resistant strains are called MRSA. Teixobactin must complete many hurdles before it can become a drug offered in the doctor’s office. It will need to be formulated to remain active inside the human body, toxicology tests will need to ensure that it does not confer nasty side effects, and experiments will need to determine other medicines it may interact with. Lewis is working with a company to improve the teixobactin’s solubility, and he estimates that it will take two years to get to clinical trials, which will then take at least another three years. So, even in the best case scenario, texiobactin will not be helping us to fight off antibiotic resistant disease for the next five years. <h2> In the Meantime </h2> Of course these are not the only promising technologies being developed to prevent, fight, and treat antibiotic resistant diseases. <a href="http://www.pbs.org/wgbh/nova/next/nature/phages-for-food-safety/"> Bacteria-targeting viruses </a> , gene editing, nanoparticles, and shotgun-like strategies using multiple drugs are all brimming with potential. But each of these needs time—time for research and development and optimization. In the meantime we will have to trust that our current technologies and common sense prevention provides the window we need. (Please, everyone, wash your hands.) As for my brush with an antibiotic-resistant infection, I eventually returned home to my husband and children. On the fifth day, lab results revealed why the drugs were not working. I did not have MRSA. I did have E. coli , but the strain I had was resistant to the drug they were giving me. Neither of the antibiotics was having any effect. The doctors had made their best guesses, but those guesses had been wrong. The hospital let me leave with new antibiotic and a tube inserted into a vein close to my heart. Don’t let that tube get dirty, they warned me, or the infection could kill you. Don’t get air in the line, they warned me, or that could kill you too. To say I was careful is an understatement. Three times a day I fed my newborn, put him down to sleep, and followed the hour-long procedure. Years of work in a nanotech laboratory had taught me how be meticulous. After two weeks, a nurse came and removed the line next to my heart. The treatment had worked. The bacteria I acquired at the hospital had not evolved resistance to every weapon in our arsenal. At least, not yet. Photo credits: <a href="https://en.wikipedia.org/wiki/File:P_vortex.PNG"> Paenigenome/Wikipedia (CC BY-SA) </a> , Oxford Nanopore Technologies

A number of promising new technologies could save us from deadly infections after we lose our best medicines.

Jenny Morber

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